Re: Alternate timelines - What can you mess with???
Well, there are plenty of cases of authors who have written works that have offended many (or certainly could) - Michael Moorcock's "Behold The Man" and Salman Rushdie's "Satanic Verses" come to mind.
All I'd say is consider the consequences in making the decision - you may lose readers, may gain readers, or may have death threats issued against you. If the consequences outweigh the benefits of having that part of the story in there, probably best to take it out.
A simple "it will offend group x" is not a reason to exclude something per se, but you do want to weigh up the consequences of offending group x in deciding whether or not to keep something. Many great ideas will be offensive to some group or other, which is why I say them taking offence is not immediate grounds for removal, otherwise a lot of stuff would simply never be written.