The Saints actually played much more 4-2, as the strength of their defense is on the DL - which is where our is as well; so it only makes sense to have those players on the field.
Perry or Neal aren't the issue here - the issue is Pickett, Raji, Hawk, and Brad Jones. 2 of those guys should not be on the field in the nickel. Pickett for sure, and one of either Hawk or Brad Jones, depending on whether the team we're playing is expected more likely to run or pass. Pass? play Jones over Hawk; Run? play Hawk over Jones.
As for Raji, at this point, I'd play him predominantly in the base 3-4, and leave the nickel interior line to Daniels, Peppers, D. Jones, Guion, Worthy, and now Thorton; with Perry used as a situational pass rusher from the DE position in a 4-2. Maybe a 4-2 of Peppers, Daniels, D. Jones, and Perry on the line. Use Boyd and Raji in the base - which we only run about 20% of the time anyway.
The goal should be to make as much use of the DL talent as possible, and minimize the use of Brad Jones and Hawk. Bradford will surely be in the mix on the outside as well.