I wouldn't consider it pejorative.
I would, though, consider it insincere. It's the kind of platitude that used to be commonplace in business communications. Rather like ending a letter with "I remain, sir, your obedient servant...".
Like earlier posters, I do not find this "pejorative". But if the context is such that they are asking for my help, then the "will" (in place of "would") would rankle, since they seem to be taking my cooperation for granted.
I think that "insincere" is rather harsh. Polite forms of address, like the modern "Pleased to meet you", are often insincere in that sense, but no one usually takes offence at it. Samuel Johnson said: you may say to a man, "Sir, I am your most humble servant." You are not his most humble servant... You may TALK in this manner; it is a mode of talking in Society: but don't THINK foolishly.
"would be appreciated" would be polite. "will be appreciated" sounds like a command or a threat. It suggests that you have some penalty in mind that you can and will impose if the addressee does not cooperate. "Tax payments are due next Tuesday. Failure to pay on time may result in seizure of your property. Your cooperation will be appreciated." See Pertinax' post.
In fact, the tax authority probably would "appreciate" your "cooperation," since it would save them the trouble of filling out paperwork, having your property condemned, and scheduling an auction.
Once upon a time, commands were given in polite, even obsequious, language. An admiral might send a note to a junior officer that he would appreciate seeing the officer "as soon as convenient." But woe to the officer for whom "convenient" was not RIGHT NOW, THIS INSTANT, and who kept the admiral waiting for even a moment longer than necessary. Both the admiral and the lieutenant knew this, of course.
While I agree with Fabulist that "Your cooperation in this regard would be highly appreciated" would be less of a command than "Your cooperation in this regard will be highly appreciated", I would still bridle at "Your cooperation in this regard would be highly appreciated."
It may work in some varieties of English. But in mine it would be decidedly irritating.
Every expression has its place, and I think this one is perfect you plan to sue the person if he doesn't cooperate. It is a strong implied threat, veiled in apparent gallantry.
To break it down, here is is why I would hate to get a letter with this sentence in it:
Cooperation The word cooperation, too often used by those in authority to those beneath them, reads to me here as "obedience." And why is it capitalized?
in this regard This is a somewhat stiff expression which comes off as legalistic and stuffy in American English.
will be as stated above, the use of the future, rather than the conditional could be read as bossy, authoritative
highly This emphasis reads to me as an additional threat. Perhaps it is not, but to my ears it is. It also may be that "highly" is more often used in BE and does not sound this way to British speakers.
passive voice The passive voice, not stating who would appreciate the cooperation, adds to the overly formal bureaucratic tone.
But no matter how nicely you write it "I would very much appreciate your cooperation in your matter", to me, this sentence to me always reads, "You had damn better do what I say or else." Sometimes that is appropriate--particularly if I actually have authority over you and I am reminding you of that. But if you write this sentence and you are not the boss of the person who is receiving it, it is likely that it will not be greatly appreciated.