Alex Smith wasn't any good until 2 things happened
1. Jim Harbaugh
2. Colin Kaepernick as his backup
Harbaugh is obviously a ninja QB master coach. Colin Kaepernick is obviously ridiculously talented and maybe drove Alex Smith to be better.
So, we still draft Geno Smith. Let them battle it out. If Alex Smith sucks here, we plug in Geno. If Alex Smith brings all of Harbaugh's teachings with him and ends up being good for us, we trade Geno for high value.