I don't sense any Mary Sue Syndrome in Celica. She's extremely, perhaps even unrealistically, kind and forgiving but that's more of a weakness than a strength, and it gets exploited. It's the friends she makes along the way who defend her from those attackers, and that is the benefit to her kindness. Also she does become a very powerful mage so that helps a lot when she needs to defend herself.
Have you ever wondered how realistic it is to combine everything that Celica does? :-)
1. Work for the guild to destroy monsters.
2. Work as part of a ship's crew.
3. Toy of several beautiful girls.
4. Representative of people in the world of other races.
5. ...
The game simply physically cannot fully show every type of activity that our blonde does. And she somehow combines it.
Yes, it is a combination of her being an actual main character (the player character) since Rule of Cool dictates it is better to involve the player than strive for realism overall, as well as camp in that the story is meant to be a half-serious fantasy world. Yet despite that, the game designer has included a silly yet fairly airtight basis to explain it: to avoid spoilers I will say only that for reasons explained later in the game, people and creatures throughout the game world feel an unnatural sexual attraction to Celica specifically, simply because of who she is.
I think that the plot, though clearly contrived, easily fits within my suspension of disbelief as the world building seems to have been diligent enough to consider these things.