Short answer to this question is ABSOLUTELY YES, you can do this. How do I know? I was in the EXACT same situation as you.
BTW, my wife is a US citizen, and I'm halfway through my FSW process after 17 years of marriage to my wife. Although we separated on friendly terms (we may stay married for a long time, since her parents are strict Catholics and do not believe in divorce), she is not willing in any way shape and form to cooperate with me for anything such as medicals, PCC etc, and she has zero intentions of leaving the United States for obvious reasons.
Cherishlady's answer is pretty much correct. My attorney helped me draft a DECLARATION which will need to be NOTARIZED, stating that I will NEVER in the future sponsor my wife and I acknowledge that, and that I would like her to be excluded from being examined for immigration purposes.
See my timeline. I got my PER, finished medicals, in the process of sending them the PCCs now. No issues or no problems whatsoever. Keep in mind however, that you will need to include her details in the generic application (just her name, date and place of marriage, date of separation). No other details are needed if you don't know them.