Kunjwal said the evidence produced by the party against Arya was insufficient, a Vidhan Sabha official said.
Arya has made no bones about his preference for Congress and was suspended by BJP for anti-party activities. The rebel MLA absented himself from the Assembly on March 18 despite a whip asking all members to be present in the House as the party wanted a division of votes on the Appropriation bill.
BJP chief whip in the Assembly Madan Kaushik had petitioned the Speaker seeking Arya's disqualification.
"The Speaker showed great hurry in disqualifying Congress MLAs under anti-defection law who went against Harish Rawat but he does not find the evidence against Arya adequate. He has acted once again like Harish Rawat's agent despite occupying a high constitutional office," Pradesh BJP spokesman Vinay Goel said in a statement.
The state Assembly has been under suspended animation ever since the state was brought under President's Rule on March 27, just a day before CM Harish Rawat was to go for a floor test in the House.