A couple of things.
1. The fact that oldBSG fans stomped off in a huff didn't hurt either the ratings or critical reception of nuBSG in the slightest.
2. Changing the gender of characters such as Starbuck and Boomer didn't hurt nuBSG in the slightest.
- In the case of Boomer, a new character (actually, many new characters) were created to occupy the spot of an original character, who basically had no character at all.
- In the case of Starbuck, making her female gave added dimension to her relationship with all of the Adamas, from Zak, to Bill, to Lee.
Getting back oldTrek vs. nuTrek, Uhura's character has only benefited from having greater dimension and definition. The Prime Universe was played out and stale. At least nuTrek is trying new things, and a careful analysis shows that they generally aren't really random new things at all. And, similarly to the situation with oldBSG, the fact that certain fans of oldTrek aren't satisfied isn't really hurting nuTrek, either at the box office or in the overall critical reception.