The general rule is such that USA does not immediately grant foreign citizens with the Permanent Residency after marriage with US citizen. Therefore, the Green Card is issued for a term of not more than 2 years. Not later than 90 days before the term expires, both spouses should submit an application for a permanent Green Card -- Form I-751 "Joint Petition to Remove the Conditional Basis of Alien's Permanent Resident Status". The failure to file Form I-751 will result in termination of permanent residence status and initiation of deportation proceedings.

If you do not submit the application, your wife loses her rights to stay in the US and is to be deported upon the expiration of her Green Card (2 years or whatever term it was originally issued). It is impossible to invalidate Green Card before its expiration date. The Green Card automatically expires upon its expiration date.

The only ground for preventing a person from entering the USA can be a crime committed by that person and criminal proceedings initiated against that person. However, all these circumstances do not prevent you from applying to court to start divorce proceedings regardless of whether your wife is in the USA or not.