You mean to say that one should not challenge an administrative decision through RTI but only through appeal or revision to appropriate court. Right?
You can not challnge the mertis of the decision even if it is administrative. You can only seek information and cannot under RTI Act ask why decision "A" is taken and why not "B".
Given facts indicate that you want to seek reasons for a decision as you feel (rightly or wrongly) as faulty. You can filed appeal before Supreme Court or the larger bench as advised by your lawyers after seeing all record. Unless wanting to run the risk of hauled up fopr contempt you can proceed.