First off I'll say don't do it and if you want a new lower, pony up the extra cash and buy one as opposed to re-anodizing.
As far as if Colt will do it... Yes they will do it but as I understand it, their re-anodizing quality is shit. Guns come out looking horrible. I do not have first hand experience with this, but people I know and trust in the industry have all said this.
What I do have first hand knowledge about is re-anodizing lowers with U.S. Anodizing. This company is ran by a man named Victor and he is the best in the business. I think Scott will forever despise me, but I actually had Victor re-anodize a Colt M16A1 lower and it came out looking amazing. Now I'm not a "how the gun looks guy" usually, but in this case I didn't buy my M16A1 as a collector, rather I bought it to try and make as close to a current production M4A1 as I could get. In order to do that, I wanted it to look new and correct, so I had Victor do it. Ended up costing me $150 I think, so much cheaper than buying a whole new lower.
As for pins not fitting, I'm not saying Scott is wrong, but that has not been my experience at all and MANY other guys in the M16 forum have done the same with their converted M16's. If anything, lowers have been reported as fitting even better. Maybe this is all just an exception for Victor because he does such amazing work.
With all of that being said, if I could do it again, I would NOT do it. After I got it all put together, I felt like it would have looked more correct if the lower and upper didn't match...
Anyway, I have to run right now, but I can post some before and after pictures later.