Joanna Cherry said it is "remarkable" Peter Murrell's SNP membership has not been suspended and said his treatment had been "very different" to other members of the party.
Cherry compared the case of the former party chief executive and Nicola Sturgeon's husband to MSP Michelle Thomson, who was suspended in 2015 over a police probe.
Cherry also said "gender crticial" feminists had been suspended by the party for their tweets.