Depending upon the privacy level of the profile, you can remove children from the profile, change the person's parents or spouse, etc. You click the "Edit" tab for the profile (after merging, presumably) and then there will be people listed in relationship slots in the right column with "edit" buttons for each type of relationship, which you can press to change the people occupying those relationships.
The thing about WikiTree, however, is that nobody owns an ancestor or that ancestor's profile. A source that one person thinks suspicious, another might find reasonable. If you know that those relationships are erroneous, you should ensure the profile is accurate - but it sounds like you don't have that level of certainty about this person. On the other hand, if the weight of the evidence is against the relationship, but you're not certain, it might be better to change the status level for the relationship to "uncertain."
EDIT: As Ms. Smith said, having proper documentation to back up whatever you do is key.