If the Church simply advocated monogamy, then the analogy would hold. But it advocates monogamy and prohibits condom use. It even prohibits condom use between two married people, even if one of them has HIV. The closest equivalent in your analogy would be if the "meat is murder" people said "You shouldn't eat meat. But if you do, make sure the animal suffers first."
I'm always puzzled by this argument. The Catholic Church doesn't teach that it is wrong to for unmarried people to use a condom while having sex, it teaches that t is wrong for unmarried people to have sex. The condom rule only applies to married people, there is no rule as to whether people who are already disregarding its teachings should be allowed to use condoms.
It makes a difference though. If people interpret all condom use as being a sin, then there is a chance they will not use them in non-marital sex, so the policy (or possibly just the lack of clarity in the policy) may still lead to increased HIV infections.
It depends on whether the prohibition on condoms does indeed increase the spread of HIV in non-monogamous sex. If it does, then the combined monogamy+no comdoms policy causes more HIV infections than a simple monogamy policy. Therefore the no condoms policy is a cause of spreading HIV. This would be equivalent to the suffering caused by vegetarians demanding that animals farmed for food should be made to suffer. They can be praised for their vegetarianism, but should still be held accountable for the suffering they cause.
