I would say that I'm most sympathetic to consequentialism and utilitarianism (if understood to allow aggregation in other ways besides summation). I don't think it's entirely implausible that the order in which harms or benefits occur can matter, and I think this could have consequences for replacement, but I haven't thought much about this, and I'm not sure such an intuition would be permitted in what's normally understood by "utilitarianism".
Maybe it would be helpful to look at intuitions that would justify replacement, rather than a specific theory. If you're a value-monistic consequentialist, treat the order of harms and benefits as irrelevant (the case for most utilitarians, I think), and you
1. accept that separate personal identities don't persist over time and accept empty individualism or open individualism (reject closed individualism),
2. take an experiential account of goods and bads (something can only be good or bad if there's a difference in subjective experiences), and
3. accept either 3.a. or 3.b., according to whether you accept empty or open individualism:
3. a. (under empty individualism) accept that it's better to bring a better off individual into existence than a worse off one (the nonidentity problem), or or,
3. b. (under open individualism) accept that it's better to have better experiences,
then it's better to replace a worse off being A with better off one B than to leave A, because the being A, if not replaced, wouldn't be the same A if left anyway. In the terms of empty individualism, there's A1 who will soon cease to exist regardless of our choice, and we're deciding between A2 and B.
A1 need not experience the harm of death (e.g. if they're killed in their sleep), and the fact that they might have wanted A2 to exist wouldn't matter (in their sleep), since that preference could never have been counted anyway since A1 never experiences the satisfaction or frustration of this preference.
For open individualism, rather than A and B, or A1, A2 and B, there's only one individual and we're just considering different experiences for that individual.
I don't think there's a very good basis for closed individualism (the persistence of separate identities over time), and it seems difficult to defend a nonexperiental account of wellbeing, especially if closed individualism is false, since I think we would have to also apply this to individuals who have long been dead, and their interests could, in principle, outweigh the interests of the living. I don't have a general proof for this last claim, and I haven't spent a great deal of time thinking about it, though, so it could be wrong.
Also, this is "all else equal", of course, which is not the case in practice; you can't expect attempting to replace people to go well.
Ways out for utilitarians
Even if you're a utilitarian, but reject 1 above, i.e. believe that separate personal identities do persist over time and take a timeless view of individual existence (an individual is still counted toward the aggregate even after they're dead), then you can avoid replacement by aggregating wellbeing over each individual's lifetime before aggregating across individuals in certain ways (e.g. average utilitarianism or critical-level utilitarianism, which of course have other problems), see "Normative population theory: A comment" by Charles Blackorby and David Donaldson.
Under closed individualism, you can also believe that killing is bad if it prevents individual lifetime utility from increasing, but also believe there's no good in adding people with good lives (or that this good is always dominated by increasing an individual's lifetime utility, all else equal), so that the killing which prevents individuals from increasing their lifetime utilities would not be compensated for by adding new people, since they add no value. However, if you accept the independence of irrelevant alternatives and that adding bad lives is bad (with the claim that adding good lives isn't good, this is the procreation asymmetry), then I think you're basically committed to the principle of antinatalism (but not necessarily the practice). Negative preference utilitarianism is an example of such a theory. "Person-affecting views and saturating counterpart relations" by Christopher Meacham describes a utilitarian theory which avoids antinatalism by rejecting the independence of irrelevant alternatives.
Inevitably, utilitarians would bite the bullet here, since ex hypothesi, there is more utility in the world in which all beings are replaced with beings with higher utility.
I think the question is whether this implication renders utilitarianism implausible. I have several observations.
(1) The assumption here of the thought experiment is that the correct way to assess moral theories is to test them against intuitions about lots of particular cases. And utilitarianism has plenty of counterintuive implications about particular cases: eg the one in the main post, the repugnant conclusion, counting sadistic pleasure, and so on ad infinitum. The problem is that I don't think this is the correct way to assess moral theories.
Many of the moral intuitions people have are best explained by the fact that those intuitions would be useful to have in the ancestral environment, rather than that they apprehend moral reality. eg incest taboos are strong across all cultures, as are beliefs that wrongdoers simply deserve punishment regardless of the benefits of punishment. These would be evolutionarily useful, which makes it hard for us to shake these beliefs. I don't think the belief that subjective wellbeing is intrinsically good is debunkable in the same way, though discussing that is beyond the scope of this post.
Analogy: the current state of moral philosophy is similar to maths if mathematicians judged mathematical proofs and theories on the basis of how intuitive they are. Thus, people's intuition against the Monty Hall Problem was thought to be a good reason to try to build an alternative theory of probability. This form of maths wouldn't get very far. By the same token, moral philosophy doesn't get far in producing agreement because it uses a predictably bad moral epistemology that overwhelmingly focuses on intuitions about particular cases.
(2) Rough outline argument:
a. Subjective experience is all that matters about the world. (Imagine a world without subjective experience - why would it matter? Imagine a world in which people complete their plans but feel nothing - why would it be good?)
b. Personal identity doesn't matter. (See Parfit. or Imagine if you were vaporised in your sleep and then a perfect clone appeared a millisecond afterwards. Why would this be bad?)
From a and b, with some plausible additional premises, you eventually end up with utilitarianism. This means you have to bite the bullet mentioned in the text, and you also find the bullet plausible because you accept a and b and the other premises.
Related to (1), I think a response to utilitarianism that started in the right way would attack these basic premises a and b, along with the other premises. eg It would try and show that something aside from subjective experience matters fundamentally.