I don't think she was a Mary Sue even in 1, just not a particularly well written character. But as for now:
She doesn't know about her own insane magical talent, though her parents, important figures like Glossaryck/Baby, and the audience do. I think she sort of views herself as kind of a fuckup-- meaning she's both likely to sell her own abilities short and unaware of the danger her magic at its worst could cause to herself and others.
I'd say the second half of S2 very much shows Star getting bitten in the ass. Her broken wand almost killed herself and Marco, on different occasions. The loss of her book allowed Toffee to come back, and obviously Star and Moon are his main targets-- not to mention Glossaryck is now working for him (obviously it's to help Star in a convoluted way but he still has more power as a result). We don't know yet what outing the family's secrets will do, but it seems pretty likely the Mewman population has lost trust in the royal family. Her getting sent home is just the cherry on top of it all.
I think we're going to be seeing her facing the consequences of these actions herself even more next season. The whole point of the "Toffee's return" stuff was that it was going on behind the scenes, and thus had to involve Moon and the MHC rather than Star, but I doubt "Star's mom fights for her" will be the template for the rest of the series.
In fact the description of the S3 premiere states Star will be going up against Ludo herself, and while it's not stated, going by the current possession situation she's probably going to run into Toffee too.