It is a little hard to grasp how much of WordPress you really want to replace.
WordPress at front-end will typically take care of following steps:
- parse the requested URL (typically “pretty”)
- determine the current context of request (query variables)
- query the required set of posts
- determine and load which theme template fits bets
- proceed to load template and have it output the posts queried
Obviously with all the usual goodies of user management and various APIs for various tasks on top. Simply put — WP does a lot of stuff.
Much of this can be disabled, customized, and overall done in different ways.
Without thorough research of specific use case it is hard to advise on which specific parts (if any) of the process should be customized and how.
In a nutshell — yes, you can get rid of WP on front end. But that get rids of a lot of valuable bits (it is used for in first place) and it depends.