The problem is that they have come to “question” their faith in college and are now planning to marry in a Baptist church. I am quite certain that this marriage will not be considered valid in the eyes of the church.
You are mistaken on this point. The Church presumes that ALL marriages are valid until shown otherwise (ie, before a formal marriage tribunal).
It would be especially so in this case, since both are Baptized and have (likely) received instruction on the nature of Matrimony (they attended CCD, right?). Usually, if a protestant marriage is found to be null, it is because the couple lacked the proper informed consent regarding the nature of the Sacrament. But this couple has probably been informed about marriage. True, they have (probably) not received the usual marriage instruction that the Church prescribes, but they are probably not ignorant of the more fundamental aspects (such as: divorce is a no-no).
FWIW, for Latin Rite Catholics, the minister of the Sacrament is not the guy in the robes, but actually the bride and groom, who mutually administer the Sacrament to each other. So, in the situation you describe, there is a strong case for valid matter, minister, intent, substance, and form - which means it could very well be (and probably would be) a perfectly valid Sacramental marriage (a Sacrament is valid if those five conditions are met).
(FWIW, the marriage would be “illicit,” because the rite was performed outside the prescribed norms of the Church, but it would still be Sacramentally valid if these five conditions were satisfied).
Should a practicing Catholic attend this wedding
In the olden (pre-V2) days, Catholics were prohibited from attending ANY non-Catholic religious service, because their presence might give the impression that the Catholic is supportive of a flawed belief system. These days, it is left to the individual to decide, so it is really up to you.
But, if I were you (being myself a traditionally-minded Catholic), I would go.