They didn't blow it trading away Thornton, they blew it getting the return they did. Blame their GM, who was only comfortable with about 5 other GMs and didn't really shop him to create a bidding war. They actually blew it by not anticipating the salary rollback, thinking the creation of a cap would leave them with tons of money to spend for elite players who other, cap-strapped teams could not sign. Instead, they lost guys like Brian Rolston, Mike Knuble, and Michael Nylander and were forced to replace them with aging junk (or just junk) like Brian Leetch, Brad Isbister, and Alexei Zhamnov. Raycroft regressed and never became the elite #1 goaltender he looked like in his Calder-winning year. They also gave Glen Murray $4M to make Joe happy, which didn't work out too well. Murray's a good garbage-collecting goal scorer (and at this point, besides maybe Sturm, the only one they have), but that money was way too much for him.
Throwing money around last offseason was not a bad idea. Zdeno Chara is a stud as a shutdown defenseman. The problem is that he is asked to do way too much; he's not going to put up 75 points for you, but if tasked with shutting down any forward in the world, he can do it; he would make Jagr constantly irrelevant during Rangers games. That said, probably would want more for $7.5M, but it's not as bad as some would say. If given the chance to be a little more physical by Dave Lewis, he'd be awesome (actually, if Lewis was fired, this team would probably be alot better... maybe then Phil Kessel would play more than Mark Mowers on any given night). He's still a true #1 defenseman, and there aren't too many of those.
The other guy they threw money at was Marc Savard ($5.1M), and most people agree that getting him for that change was a steal. Savard is a better pivot than Thornton (note I said better pivot, not a better player) and the best passer I've seen since Adam Oates. Savard's the best player on the team and was worth every penny (and more).
That said, the Bruins have some good young talent. Bergeron is still one of the best young two-way centers in the league, and will probably be a more talented Chris Drury at his peak. Phil Kessel will be a world-beater sooner rather than later (a Mike Modano with a better shot who can also play wing, rated 6th best prospect in the world by hockeysfuture.com), but he is only 19 still and has alot of growing to do and despite that was still the Bruins best forward for the last month and a half or so of the season. Tuukka Rask looks like a future top 5 goaltender (he's rated as the 7th best prospect in the world and the best goaltender by hockeysfuture.com), and Hannu Toivonen could be a late bloomer like two guys his skill set resembles quite a bit, Jean-Sebastien Giguere and Ryan Miller. Brad Marchand and Milan Lucic, two picks last year, played extremely well in the Q and W respectively this year, Lucic leading his team to a Memorial Cup berth and being the type of gritty, skilled power forward that could remind some of Terry O'Reilly. Petr Kalus and David Krejci both looked very good in Providence this year and in their limited time with the Big B's, and Matt Lashoff and Mark Stuart did as well (Stuart will likely be the #4 D or so next year for Boston). With the 8th overall pick this year, they should be able to pick up a guy like Logan Couture or Sam Gagner who will add to this stable (or maybe Alexei Cherepanov, though the lack of a Russian transfer agreement makes any pick there risky).
The Bruins aren't screwed. They have a good stable of prospects. But they'll be technically irrelevant for a couple more years until these guys develop. By that time, Chara and Savard will still be in their primes.
