They wouldn't just be picketing the funeral of a homophobe though, they'd be picketing the funeral of someone who organized and funded a group that picketed thousands of funerals of people who died in far more tragic ways than going out naturally in your old age
Fair enough, but I don't see that as a meaningful difference. "Picketing funerals is a pretty shitty thing to do" seems like the basic reason to be opposed to Phelps, not "picketing funerals of unrelated people who died at war is a shitty thing to do".
Granted, if someone's opposition to Phelps was strictly that he picketed military funerals over gay rights, as opposed to that he picketed funerals at all, sure, they're not being hypocrites*. I find it hard to accept that Phelps' problem was solely that he picketed the wrong funerals for the wrong reason and if he had chosen a suitably horrible dead person and a different cause we would all be cheering right next to him, though.
*Also known as the "You can't fail to honour your principles if you don't have any" defence against hypocrisy.