don't do it man. if there is a conflict of interest, then there is a conflict of interest, period. it doesn't matter if they are offering you $3000 or $300, a low amount of money doesn't 'resolve' the conflict of interest...in fact it makes it worse as they are not offering you a fair market price when the work being done is outside your job description.
Personally I'd just politely refuse, say thanks, that you understand their position but the amount they are offering is not within the fair market value of your work. Thank them for their time and interest. Don't even put in a counter offer, because that will just make things worse if they think your counter offer is too high (which they will based off what they are offering). And for the love of all things good in this world, don't tell them that you're working on making your photography a career, this is your current employer, nothing good can come from telling them your future plans to make money outside their timeclock. Be professional and polite and succinct, but don't apologize for not taking the job either, you're not at fault for them having to look elsewhere for the service, they're the ones who are at fault for losing the job for not offering you a fair price. You could even find the most ridiculously expensive commercial photographer you can, and without saying anything, just toss a casual reference to them so that if they go to them for a quote, they'll get an incredibly expensive price, and that may have them re-think their position (probably not, but hey why not)
If they come back and reply to that and say they are still interested and WANT a counter offer, then give them a straightforward price like tiredon gave, and if needed, explain your costs and man hours involved (i.e. equipment costs, travel costs, prep time, shooting time, production time, and if you're off the clock during any of it, than this is YOUR time, not theirs. they can't have it for free) and where your numbers come from and if needed perhaps provide some examples from credible sources like have been linked to in this thread already, they are business people, not photographers, they'll understand and appreciate numbers and cold hard facts.
but personally, I'd just walk away....You should Nancy Regan this whole situation and just say no.