I had to do the same to a Hyside with white hypalon paint on the side for the outfitters logo. I used Toluene and some sort of scraper. Nothing sharp that would puncture the boat. What worked best was toluene on a rag. I would wet the paint with toluene, let it sit for maybe 30 seconds, then rewet with toluene. It would usually take several applications. I was just wetting the paint with the rag, not scrubbing. After a few applications the paint starts to soften and you could start to scrape it. As soon as the paint starts to dry out you'll need to rewet with toluene, which happens often because the toluene dries out quickly. If you can work out of direct sunlight the toluene wont dry off as fast. Be sure to wear a respirator and gloves. That stuff is nasty.
I know what you are saying about the chemicals cleaning up the raft just by where your working. Don't sweat that too much. I used Inflatable Boat Cleaner to clean up the rest of the raft, then fresh 303 everywhere, and it blended well enough.
It took me several tedious days to get it all off. In the end it was a total pain, but it worked. If I had it to do over again I would have seriously considered just gluing a patch over the company logo to cover it.