As someone who's both paid and fought this fine a half dozen times each, first let me say I'm sorry!
Now a bit of advice: so long as you stay in a place better than a shit bag, always use the free shower cap to cover the smoke detector - the #1 way to get this fine is to turn a room into the ark of the covenant full of blunt smoke. Tip 2 is to slap that ma'fuggin 'do not distrub' tag on your door handle from the moment you walk in. Tip 3 is run the shower when you blaze and if you have a bathroom vent fan, get that rockin. Of course, open the windows is a no-brainer, but not an option in Las Vegas, Atlantic City, or anywhere else people might be inspired to jump to their death after blowing their life savings. That said, in Vegas, I've had the housekeeper tastefully arrange my stash/papers/grinder/broken up bud on a tray while I was out - often, if you tip everyone well, they realize it's in their best interest to keep you there and keep you happy rather than get you fucked and get the company paid.
Sounds like you're getting fucked with though - not nearly as black and white as the smoke alarm going off. You need to call them and be painfully nice; ask for the manager and tell them (remember - stay painfully nice!) that you're extremely frustrated with some of the hotel's charges. If you're in a medical marijuana state, inform them that was your medicine and you had broken it up to make medicated tea. If not, that was herbal incense until they get a GC/MS lab test that proves otherwise.
Make sure to tell them how frequently you travel and enjoy the comfort, service, and privacy that Marriott has always provided--so much so, in fact, that you've chosen a Marriott by your home to be the location for your 200-guest wedding. To be completely honest, though, you feel that this entire process has been both invasive and embarrassing and you want to make sure that this was just a one-time misunderstanding and doesn't represent a collapse of Marriott's quality.
If that don't work, go the credit card route. If you're *really* good at playing the role, it's possible to get a free room next time you travel out of the deal, but you should be satisfied with the smoking fine being removed.
Oh - and for your amusement - most I've ever paid in a smoking fine in a hotel was $500 to the Mark Hopkins International in San Fran (smoke alarm went off, they had to remove it, clean it, reinstall it, STILL went off, then they disabled the alarm for our room and we cheefed it the hell out!)