If the repair is statically acceptable and the durability is adequate, then it is OK. I usually try to get a minimum of three rows for fastener load distribution. However, compliance to the FARs is what you are after, as long as you check the durability of the two rows and implement supplemental inspections as necessary, you are good.
One issue is that you may only be adding two rows due to interference with other structure. Possibly using two rows of larger dia or hi-loks in lieu of rivets, etc.... if this is the case then make sure you don't superimpose stress concentrations. Ending two parts in close vicinity can really emphasis the bending at the end rows. If you only are putting two rows because the part ends, just cut the whole section out and only have one splice.