What I want to know is are these two sides balanced?
Does it matter?
Inquisitor is not 40k; it's not a game of balanced armies; it's not necessarily fair - sometimes you're the underdog and are totally outclassed by your opponent. It's about telling a story, or in your case, re-telling a story. You as GM are there to make sure both players have fun so don't be afraid to ignore the rules if it'll make for a more interesting story and/or game.
That all said, a couple of things that jump out at me. Firstly, Bequin should have the
Pariah ability, it's in the Sergeant Black article which you can find a copy of if you look at MarcoSkoll's sig on Warseer (you'll also find that Warseer has a more active
Inquisitor community than here). Secondly Mandragore could probably take on Eisenhorn's warband in a straight fight with one hand tied behind his back - this is as it should be, and figuring out how to deal with Mandragore will be the real challenge for whoever plays Eisenhorn - so much so that I suggest you play the scenario through a couple of times, taking it in turns to play each side and GM.
I would be tempted though to play a more simple game first - perhaps a gunfighter like Slick vs an enforcer like Barbaretta, just to get used to the rules and how actions, shooting, combat and injuries work. As it is, you're jumping in at the deep end a little with some powerful characters with quite a few special rules and it might be too much to take in in one go. After a 1v1 I'd try a scenario something like Slick and Barbaretta vs a GM controlled marine to give you a chance to see just how powerful marines are.
Any other questions, let me know.
- Dave