But once you create such a system and decide that questions such as these will be decided by referendum, it becomes a logical conclusion that referendums can also overrule earlier referendums if popular opinion has changed in the meantime.

I will admit that it would make sense if there were requirements of a minimum amount of time that has to be between two referendums on the same topic - so as not to waste everyone's time and resources asking the same question time and again - but on the other hand, if there are no such requirements, you can't blame the supporters of gay marriage if they keep trying. And since opposition to it would likely diminish rather fast once it became legal and the opponents realized how its existence didn't affect them in the slightest, I should imagine that once it gets passed, it's unlikely that attempts to repeal it again would work.

Of course, the same goes for many other potential questions, and so it really would not be a bad idea to implement said requirements... but afaik they don't exist now.

Referendums are always a tricky business, honestly, and they're definitely not the best medium through which to decide on most political questions. But on the other hand, considering that there are rather few serious arguments against gay marriage and it's merely a matter of waiting until any given society is ready to accept it, I suppose it makes a certain amount of sense to cut out the middleman, the Californian state house and senate, and put it to the people directly to see if they're ready or not.