They did trade away young players, but I think the overall organizational philosophy was to simply use the farm system to make trades, not to develop or acquire players.
It is not just that they traded away prospects, it seems like they neglected player development as a means to improve the big club.
Ulitimately, their approach was very half-assed. If you are going to build through free agency they should have had the guts to sign a Vlad to really pair with Bonds. Or even Tejada. If you are going to go so far as to sign FAs that will cause you to lose draft picks (Michael Tucker), they might as well be bonafide starters.
They should have been able to incorporate one or two home grown position players into the team from 03 to 07. It would have saved a lot of the money they ended up spending on vets like Alfonzo.