Hm. My intuition says it doesn't balance, but of course this will depend on the specifics of the disease, so you could be right. We can also assume you can construct some disease such that the possibility of surviving it without the vaccine is similar to the possibility of surviving the apocalypse without a bunker.

But that's besides the point. I think this argument doesn't really work because to be consistent, you have to prefer suicide to living in a post-(apocalypse, infection) world. Or rather, it does work, but only for really extreme situations. Vaccines are typically much less expensive than bunkers, so the cost of deferring your suicide decision is much less (although you may not want to if e.g. the disease leaves people paralyzed).