Thompson is a very good drafting GM after the 1st round, but in the 1st round he's as much at the mercy of the draft board as anyone else. Most late 1sts flop, the quality of those picks is nowhere near as good as a top 15 pick most years. It's the same exact thing with JS. JS is average in round 1, but superb after that. Any team that is above average in round 1 (the Rams) is drafting high every single year. Give the Rams nothing but late 1sts and their 1st round picks would look underwhelming too.
Thompson has rarely ventured into free agency, but when he has he's done very well (Peppers, Woodson). His philosophies about building the team through the draft and spending money to keep proven in house talent is the smartest way to build a cost-effective roster, and it's also exactly what JS does.
The difference is, I'm not really seeing what McCarthy and his coaching staff can bring to the table as talent developers. John Schneider has Pete Carroll: hands down the best talent developer in the NFL.
I see McCarthy as the hindrance, not Thompson. And that's not even getting into McCarthy's well documented issues with playcalling and in-game decisions. Put Pete Carroll on that team and within a year or two they could be the team to beat in the NFL. They won't get a guy like Carroll, but upgrading from McCarthy could still make a positive difference.
Football is so much more about coaching than acquisition. USC has dominated recruiting going back ages, but only became a serious contender with Pete Carroll. UCLA was even worse, posting losing records with top 15 recruiting classes, before Jim Mora showed up and upgraded the coaching position. And look at how awful SF was before and after Jim Harbaugh with the same GM in place the whole time. And then look at Michigan, or Stanford, before Harbaugh showed up.
We should thank our lucky stars we have Pete. Most teams are not nearly as fortunate.