Virtually all law is at its core a legislation of morality. For example - laws against murder are a legislation of the moral law “thou shalt not kill.” Your federalism concerns would be appropriate if we were trying to use the courts to impose a ban on gay marriage - like the liberals did with abortion. However, we are talking about a constitutional amendment here. Constitutional amendments are by definition constitutional and thus are not subject to concerns about federalism.
The fact remains, the federal government should not be deciding this issue. They tried it with alocohol....what did that accomplish? There is a reason why the founding fathers made it hard to amend the constitution. They were sheer visionaries in that aspect. This is a culture war issue that needs to be decided at the state level, not the federal level.