No.
Longer version: No. The option is there for those who want to use it and for those who don't, then simply don't do it.
I time travel all the time for my own reasons and I feel absolutely no guilt. I honestly don't understand why anyone would.
I still enjoy the game. I still like to occasionally talk to villagers after completing all tasks. And, most of the time, I get more enjoyment time traveling than I do playing regularly: I unlock more, do more and experience more.
Maybe if the villagers had more dialogue, had different moods and personalities and weren't all butchered versions of their previous selves I'd spend the whole day talking to villagers and running errands like I used to in other AC. After a while of talking to villagers in New Leaf though, it gets boring, they start repeating the same phrases and it's rare if they get mad or act mean. So basically it feels like talking to a village of clones. So most of my enjoyment derives from unlocking stuff or decorating.
I've time traveled in all of the AC games I've played: still enjoyed them; still a fan of ac--Only in the past versions the reason I time traveled less was because the villagers were actually interesting to talk to.
That's just me though.
And I'd like to know why anyone would feel guilt over time traveling in a video game or get mad if someone else does it. I just can't wrap my head around the reasoning.