I'm rolling another Orc character that strictly follows the the code of Malacath.
I was considering doing the companions quest line as that is a warriors guild.
But would becoming a werewolf interfere with the my worship of malacath?

Sure the werewolf is a strong creature that would please Malacath but they are the creatures of Hercine,if I'm not misstaken.
So do you think that becoming a creature that hunts for Hercine interfere with my worship of Malacath?

Well, the main issue some of the companions are having is that they realize that being a werewolf brings you closer enough to Hircine that when you die you'll end up at the hunting grounds. Between two daedric princes, I'm not sure which will take precedence, but can't you get cured? I've never tried.

Seeing as I allied myself to all Daedric Princes, I'm interested about what will happen when I die. ^^

if you read the 16 accords of madness:
http://www.uesp.net/wiki/Lore:16_Accords_of_Madness

Yes you can get cured,I just didn't really want to get the cure if I didn't have too.

My orc has not joined the companions but follows the codes strictly for Malacath. Even married an orc. To bad no orc babies.

But on the topic of werewolves its a toss up. Werewolves are a physical representation of power and strength. Something an orc respects. Orcs like to hunt so... hircine's hunting grounds wouldn't be bad.

Hircine would have claim of the soul. Harbinger said it taints the very soul so I think Hircine would have higher stake on you.

Still the dilemma.
An Orc would love the power a werewolf would give him but the problem with his soul going to Hircine.
I could allways get cured but my Orc doesn't know this when you accept the blood offering.

So it probably looks like the companions quest won't be suitable for this character.

thing is you don't know about your soul going to Hircine either until talking to Kodlak for his cure. So in RP sense you could have him become one and realize afterwards about the curse.

But the question is... if your Orc becomes dragonborn. who gets your soul then? Or are you the first orc to die and go to Sovngard?