It doesn't seem quite right to me that factions would give up their precious blueprints as a reward for a commission. Blueprints require Orbital Works to make use of and if you have one of those, you are likely competing with the faction in question economically.
Disclaimer: I have yet to go through faction commissions myself, so I may get this wrong....
One possible example solution is at a high enough reputation, open up the ability to create a mostly independent, satellite colony of that faction. With various advantages and disadvantages:
Negatives:
-A percentage of your colony income (eg 20%) is paid to parent faction.
-As your colony is part of a faction, expeditions are now open hostilities with those factions enemies and larger as a result.
-Since the colony is technically an extension of a faction, if relations go south with the parent faction at a later date, they will attempt reclaim your/their colony. If they are successful, control is automatically handed over to that parent faction and you lose that colony. To make this quite a bit more challenging, local security forces will stay loyal to parent faction, so it's you and your colony against everything else in the system if you try to declare independence.
Positives:
-Access to faction specific ship blueprint packs and a few common ones (eg Hegemony would give XIV ship blueprints, Hegemony Auxiliary, and Low-tech).
-Reduced costs of buildings; your parent faction will help you get off the ground.
-More profitable exports to that parent factions colonies.
-No Tariffs to pay (and perhaps a discount on purchasing ships) when trading at that factions colonies.
-Be able to request the parent factions aid in defeating an expedition.
In saying all of this, I do like the idea of having special quest missions that have guaranteed blueprint rewards. These mission blueprints would not be obtainable elsewhere by salvaging, so you need to complete that mission (or mission chain) in order to get access to that blueprint.