Katie Holmes isn't just parting ways with A-list husband Tom Cruise, she is also divorcing the Church of Scientology.

Holmes is seeking sole custody of their daughter reportedly in part to extricate Suri, 6, from her father's faith before Suri's heavy-duty Scientology education starts.

But according to multiple insiders and experts, it could be a rough ride for the former "Dawson's Creek" star, both personally and professionally.

Mark "Marty" Rathbun, a former higher-up in the church who left and became one of its biggest critics, used to be Cruise's Scientology auditor and legal affairs advisor. Rathbun told FOX411's Pop Tarts column that Holmes has reason to be concerned. 

"In the long run, Tom - if he takes (David) Miscavige's advice - may very well try to hamper Katie's career through Scientology Inc. propaganda and smear tactics after the smoke settles on the divorce," Rathbun said.