Combining InnoDB with MyISAM
As long as you recognize the tradeoffs you're making, there is nothing inherently "wrong" about introducing a MyISAM table into a primarily InnoDB database for the purposes of supporting full-text searches.

Tradeoffs:


No enforcement of referential integrity on MyISAM tables. Referential integrity may be enforced at the application level instead if this is critically important.
Database has a mix of InnoDB and MyISAM storage engines which may go unnoticed or cause confusion for future developers and DBAs. At worst, an enterprising dev or DBA may try to "improve" the schema by changing the MyISAM table to InnoDB, thereby breaking full-text searching the application.
MyISAM full text search requires MySQL-specific SQL syntax which will reduce the portability of your application.