Will denied SF85 prevent future clearance?

There was a restructuring at my current office after I had already submitted an SF85P and my company no longer is pushing my application forward. My application will now most likely be denied due to lack of fingerprint submission.

My question is this: will it be more difficult for me obtain clearance in the future now that I have been denied already?

You are using the wrong terminology. You were not denied; your investigation was either never submitted, rejected back for not meeting the FP requirement or was discontinued. This has no bearing on future applications.