I don't have a problem with time travel stories either although I was never a fan of the TCW storylines. With respect to Ent's space Nazi's, if they had not gone back to 1940's Earth and had just dropped them into a different century or decade, I would have questioned using them too. But that didn't happen. By incorporating a story which involved traveling back to the time of the Nazi's, I thought their use was appropriate.
I also loved that use of the Nazi's at the start of the season set up a very nice ironic bookend for Terra Prime/Demons', exploration of man's natural propensity for hatred and distrust of those who are different -- even "enlightened" 22nd century man.