Can I have the pen Pockets removed from my OCP uniform?

If memory serves, alterations such as this could/would be in violation of the regulations. What I found in AR 670-1 in Section 1-6(b): "No item governed by this regulation will be altered in any way that changes the basic design, or the intended concept of fit, as described in AR 700–84, including plating, smoothing, or removing detailed features of metal items, or otherwise altering the color or appearance"

Keep in mind that those uniforms are designed to be used in combat. While you may not be using that pocket now, it could change in the future.

Are you DA or CS Army? if not they in is out of regulation to modify any prescribed uniform or equipment. If it is field equipment, then you damn well better a normal set for inspections.