Since the SD50 doesn't have ditch lights could individual control of the marker lights be achieved thru wiring the markers to run off the ditch light outputs on a PS2 or PS3 board?
That would probably be inadvisable for two reasons.
First, the idea of rewiring a perfectly functional engine to achieve a relatively minuscule improvement undertakes risk for just about 0 gain. If the OP can't urn off the markers, what's the tragedy?
Second, the correct solution, which is noninvasive, is to load a sound file to remedy the problem. Assuming that the omitted soft key is an oversight and the engine's PS2 board is capable of managing the marker lights, which I pretty much believe is the case, then loading almost any diesel 3 volt PS2 sound file that has an LMK soft key would solve the problem.
I have my markers on my LokSound equipped locomotives
What's a LokSound locomotive?