I don't know where you get "misogyny" from it.
In the first season there isn't one positive or even neutral female character, not one out of Gwen, Toshiko and Suzie. Toshiko was pathetic, Gwen was a total bi*th and Suzie was evil. The only negative male character was Owen.
In the very first episode we have Owen using his very morally questionable spray to get laid. At most he got a raised eyebrow from Jack.
There's the woman as a sexual predator, who even prays on gay men who tell her no.
Then there's the portrayal of lesbianism in the first season. On both of the two occasions, it was instigated by a different woman possessed by a different evil alien. In fact I'm not sure this was improved upon in season two, where the two victorian Torchwood women (who were shown to bring our hero Jack to heel) were portrayed as evil lesbians.
The women were less sexualized overall, which doesn't seem consistent with a charge of misogyny.
Less sexualised? We had Gwen being being snogged by another woman while the men sat back and were entertained. We also had the infamous Cyberwoman, whose "outfit" made Seven of Nine's look positively progressive.