This is a rather touchy topic given she has been in the news of late.
From what I heard, the show got rid of her because Paramount/UPN weren't willing to expand the budget (I presume they did a little, assuming Ryan was paid more than Lien), so someone had to go. First it was Wang, but a certain magazine saved his hide, so next up was Lien. Really, the only other potential fodder would be Neelix, and given how central the mess hall is (ship cafeteria) to scenes, it was unlikely he could be cut. Kes was just second fiddle in Sickbay and the cargo bay set was being replaced with Seven's Borgified cargo bay. If they got rid of Wang, I'm not sure who they planned to be an Ops. Random yellowshirt? There's no conspiracy, just new castmember + hard cap on the number of castmembers. And evidently it wasn't handled like DS9, where they could load up on supporting characters, some of whom appeared more than billed actors (i.e. Lofton).
As for her change, she was a minor actor who was out of the limelight for many years. For a lot of actors, one show is their only time in the spotlight and after that, they go back to obscurity. Look at Gabrielle from Xena for example (Renee O'Connor). Sidekick in every (?) episode of the top syndicated series for several years. And after that? Look at some of the movies she was in. Didn't star in much tv since. Even a show like Voyager, highest-rated show on UPN every show it was on (behind Smackdown, which I guess qualifies as a scripted show) didn't exactly send its cast onto great success (only Jeri Ryan seems to have continued her career, at least onto 2 series in the '00s). Heck, a lot of main actors disappear. The guy in Pretender? The guy in Highlander? How about some of the cast of Buffy, Angel, and Dawson's Creek, though WB was better at churning out actors able to get more gigs (Geller, Hannigan, Boreanz or however its spelled, Holmes). If you look closely, you'll notice a lot of castmembers of shows just fade away into the background.
Oh, they did load up with supporting characters on Voyager too. We had to stand characters like Vorik, Naomi and Icheb and they became more than just supporting characters. No problem with money when it came to them.
Funny that you did mention Gabrielle which is another favorite of mine. In fact, Renee O'Connor is one of the very few actors I could imagine in the role as Kes if the character was brought back in some way in a future movie or series if Lien wouldn't or couldn't participate.
Renee O'Connor seems to be doing well after all even if she isn't in the spotlight in the same way as before. She's been involved in a lot of movie work lately.
As for the Voyager actors, it's only Ryan who have had anything like a career after Voyager. Picardo and Mulgrew show up from time to time in some series or show but where are the others?
I guess that it's more difficult for actors on TV shows to keep up the work with different roles than it is for movie actors. TV shows often lasts for years and years and the actors "become" the characters. Look at Ed O'Neill and Larry Hagman. Can anyone think of anything but Al Bundy and J.R. Ewing wjhen they show up on screen. Not to mention many of our dear Star Trek favorites.