You need to be truthful about everything on any immigration form that you file. The fact that you and your soon to be ex-wife are separated and going through a divorce makes your case more complicated but not impossible. If your wife is willing to sign the I-751 she should and you should timely file it. If the divorce becomes final during while the application is pending you would need to notify USCIS immediately. There is case law which stated that even if the parties are separated a joint petition can be filed as the present viability of a marriage is not an issue in the adjudication of a Petition to Remove the Conditions on Residence. Either way this is certainly a case where you need a lawyer.
This is a repost. See my previous answer the same question below.
Behar Intl. Counsel 619.234.5962 Kindly be advised that the answer above is only general in nature cannot be construed as legal advice, given that not enough facts are known. It is your responsibility to retain a lawyer to analyze the facts specific to your particular situation in order to give you specific advice. Specific answers will require cognizance of all pertinent facts about your case. Any answers offered on Avvo are of a general nature only, and are not meant to create an attorney-client relationship.