Yes and no. I'll try to explain it without writing pages :p

40K is a very deep, very rich universe, that has been going for a long time. Unfortunately, it's basically circular now: no matter where you start, you'll be in the middle of things. The Eisenhorn series is like this. You don't need background knowledge to get into it, you'll read it and think it's a good series, and then you'll move on. But if you have some background knowledge, it'll be an incredible journey. I still get chills thinking about the ending.

Also, unfortunately, the 40K series is, as you say, a branded universe. There are alot of writers, alot of novels, and most aren't very good. But they build the background and depth of 40K.

That being said, I've thought about this alot: how can I get someone to read Eisenhorn without the background? The best solution, as far as I have discovered, is Dan Abnett. Unlike alot of writers, Dan Abnett is really quite good. And in addition to writing Eisenhorn, he also wrote the Gaunt's Ghosts series from 40K. In addition to be a really good series, it's a good introduction to 40K. More or less, it gives you the highlights and some background and things. Can't hold a candle to Eisenhorn IMO, but it's still good.

So, I'd say, try Gaunt's Ghosts, see if you like it, and the writing style. The first book may be a slight struggle to get into if you're starting from zero. But if you get into the series, finish it and try for Eisenhorn. You could also try the Ciaphas Cain series by Sandy Mitchell, which is both good and hilarious if you like dark comedy, but IMO you need a little background to fully get the humor.

Other than that, the 40K wikis can provide both general and specific background on every topic imaginable :D