It depends on the situation. The game may not give light side/dark side points for some Dominate Mind choices, but for the element of rp, if you are into that, it can matter. If you are using it to take advantage of someone it could be dark, but to get past an obstacle the way Obi-Wan had with storm troopers for a end means of a greater good, it wouldn't be dark.
Force Persuading a Czerka official out of paying docking fees might be all right because you refuse to give credits to a corrupt and evil organization. However using Force Persuade to not have to pay Manaan their fees is a form of theft, so it should not be used there by a conscientious Jedi, though regular persuasion is fine.
One situation is where you can Force persuade Sharina Fizark on Tatooine to give the wraid plate to sell to Fasa, but that's kind of skeevy, imo, even if you were to give her the max of 700 credits after selling it. The better to normal persuade her into trusting you. Even my darksider prefers regular persuasion, unless it is to terrorize people with Dominate Mind. He a complete jerk anyways, lol.
Persuasion skill is generally fair game because the other person's free will remains intact, and if you don't have the intention of exploiting them. A light sided Jedi should focus on persuasion, since Jedi are supposedly peace keepers and diplomatic anyways. Force persuasion should be used as a last resort, although you should always pick the two Force persuade powers because you never know what you are going to run into, like Obi Wan with the storm troopers.
Persuade is the most important skill in KOTOR, imo. And you can't neglect the two mind powers