What part was bad about it for him, is your question?
The part where he didn't pull out the cocktails like in IM3 essentially. He was affected by it, plain an simple. Moreover unlike Batman who was affected by death and killing at a young age and vow'd against it there(
still going on to kill his enemies in all 3 of this new movies), Superman never faced the issue in his life before and now that he has he feels a certain way about it. Thus the answer to your question.
It's not about what's bad about something, people aren't dogs that need to be giving reward or punishment before they can grow.
You can extrapolate all you want about what YOU thought it meant(he's the last of his kind) but to then critique the film based on your assumption knowing full well that the people you are disagreeing with see it differently, seems pointless.
That would be like saying superman wants to kill as many people as possible and because of that, the film kinda fails. Well perhaps you need to prove that point first before using it. Why does superman mourn. For starters, unless JorEl suggested he kill the other kryptonians with his singularity(which wouldn't kill superman by the way).....pretty sure he doesn't think he's the last of his race.
And as for that interview, Snyder actually reiterated what I just said. He went onto say that this is now a world where the audience won't think it's an absolute impossibility that death won't occur and it will add a much needed edge to superman conflicts(as it does with every other super hero movie not named Batman in the 60's), Never did he once say it will happen again. Everything points to it never happening again actually, but if you must....