Engine oil gets dark mostly as a result of the carbon of all of the explosions happening nearby, which filters try to remove as much of as possible. Transmissions, however, don't have these carbon sources, so the darker fluid is either a result of age or heat. Heat isn't necessarily a problem unless it's excessive and your darker fluid isn't a huge surprise since towing generates more heat. The cooler's purpose is to lower overall temperatures so you can run it harder, longer. This diagram is my favorite way of thinking about transmission heat and it's effect:
In either case, the transmission filter won't help since it can't filter out the causes of the dark fluid. The filter's purpose is to pull things like fine metal shavings and other solids which are the result of normal wear and tear of a transmission. Pulling these bits out of circulation will prevent them from being run through the gears and acting as an abrasive.
All that to say it'd probably be prudent to change the oil soon and install a transmission fluid temperature gauge if you plan on towing again. A temperature gauge is always a good idea when towing so you can keep an eye on the temps and make sure things aren't getting too out of hand. If you don't tow often and/or don't have a good place for the gauge, maybe set it up so it can be disconnected quickly and maybe just velcro it to the dash.
Sorry, probably way more of a response than you were looking for

I just learned all of this recently, so it's fresh in my mind!