A pro would definitely do a better job than an inexperienced amateur, plus they have the tools to measure the clear coat thickness and know how aggressive they can get with the repair. They might suggest a respray though. As for brands of polish and compounds, pretty much anything works pretty well enough if it is brand name. This includes Mothers, Meguiars, etc. I've used Sonax which is reasonably high end and didn't see any noticeable difference.
For the silicone, just use a tube of it, cut the hole in the tip close to the size of the holes and fill the holes. It does sink in a little, just get a good thick glob in there and then smooth it out after. You'll likely end up with excess on the paint but you can probably peel that off with a fingernail if needed once it dries if you can't get it cleaned up nicely when wet.
Thanks for the info. The tube of silicone blew out the back end when I loaded it into the caulk gun, so I was just using my fingers to apply it, but it still kept collapsing into the holes. I'll give it another shot.