I didn't get your questions properly, but I presume your basic question is are hybdridization theory and molecular orbital theory incompatible with each other?
This is tricky to answer. I can refer you to Jonathan Clayden's book on Organic Chemistry, where the author took the standpoint that " there is no contradiction! " . Always remember, hybridization is only a mathematical model. If you agree with hybridization theory, then it is compatible with molecular orbital theory. The molecular orbital theory speaks of the interaction of atomic orbitals to form molecular orbitals. Essentially, there is no restriction on the fact that you may first apply hybridization to get hybridized oribitals, and then make these hybrid orbitals interact via MOT approach. This is the approach taken in many books, including in Clayden's organic chemistry. There is nothing wrong with the approach if one agrees with hybridization. Hybridization speaks of atomic orbitals, molecular orbital theory speaks of interaction between AOs, regardless of the fact whether they are hybridized or not.
However, there is an if. The if is important because there are just too many evidences against hybridization theory. I refuse to accept a mathematical approach which when tried to correlate to physical evidences, contradict recklessly! If hybridization really occurred, then there would be something like sp, sp2 or sp3 emission lines. Have you ever heard of hybrid emission lines?