no, i don't think they weren't working against sloane. if you remember, sark worked for irina b4 she turned herself in. then he worked for sloane at SD-6. when sloane and sark extracted her, sark's loyalty was back w/her. also, sloane was going to sell all his contacts and rambaldi artifacts to irina. i think it went like this:
SLOANE: What if I told you that I wanted you to buy me out? That I'd be willing to sell you the breath of my assets, my contacts, all the Rambaldi artifacts I've acquired over the last thirty years, everything?
IRINA: I'd say that either you're setting me up to kill me or I underestimated your love for your wife.
SLOANE: Well, I'm going back to Tuscany to see Emily. The house is safe. Emily's meeting me there. I'll bring the database with me, you can pick it up from me there. I can't blame Emily, she's right. I want out.
so, with those ideas in her mind, i don't think that irina would just walk in with no back up if she thought sloane was going to kill her. even irina knows sloane's tricky nature, and the part about emily could have been a lie to lure her to the villa. also, in the end, they saved his life, taking him in the copter w/ them. they could have easily just left him there to be shot.