kcode,
I have the same gripe about my CS45. The frame is anodized and any modification to the surface will break through and leave a bright silver color where the bare aluminum is exposed. On a black framed gun it will stand out very noticeably.
I called Smith & Wesson and their customer service rep told me they have a policy in place to not refinish aluminum frames

I find this highly unlikely (calling S&W is like calling the DMV, you get a different answer every time) but you would do best to have an alternate plan for the anodize process other than S&W.
A very important note is that all the frame markings might go a bit soft (especially if bead-blasted instead of chemically stripped) and the white color of the text will be lost. Laser marking burns through the black anodize and reacts with the base metal hence the lighter color.
The bottom line is that if you can't live with the bright metal where you modify the frame make sure you have a good plan in place before you perform the modification. Talk with the refinishing shop about pin holes changing dimensions, the text on the frame, and the final color and toughness of the finish (I would suggest a Type 3 Class 2 'Hard' anodize in black). The frame must be
completely stripped of all other parts pins etc. Will the shop do that or can you handle it? If the shop is to do the work how much do they charge and will they charge again to reassemble the gun?
Lots to think about. I can tell you from experience it helps to soften the edge on the trigger guard but the refinishing adds considerable expense to the project.