Quite so. You are the representation of the ruinous powers at the table.
Equally, "you serve a different god therefore I must kill you" is a bit childish. He's sworn to complete this task, whatever it takes, invoking the name of Nurgleh in the process, and if he has to put up with someone who annoys him....well, deal with it. Even Kharneth's pet psychotic kept his chainaxe to himself.
If he wants to kill the champion of an opposed power after they've done everything his brethren needs them to do, tell him to go right ahead. I doubt anyone would stop him. But don't do so in a way or at a time that risks completion of the compact.
And yes, 'everything you need them to do' includes needing the sorceror or his allies further down the line. If the heretics have a reputation for murdering their allies once the dust settles (or even before), then guess what? No-one will assist them.
If you want to underscore the point, have a Nurglesque heretic refuse to deal with them because he doesn't trust them.
Ultimately, this is no different to D&D "I'm just playing my alignment" complaints. Nurgle likes it when plague is spread, and tzeenchian champions die, and worlds lose hope. But he favours the champions who do so with a bit of panache, and keep the oaths they swear in his name (Tzeench may betray his own, but that's one of many despicable properties of Tzeenchian heretics...). Alignment in Black Crusade is no more proscriptive (in fact less so) than D&D.