Can sending correct data via UART qualify as valid manchester encoding?
The success of this scheme will be highly dependant on the drive electronics in the laser pointer module, it's impossible to guess the ramp-up and down times, but easy enough to characterise with a scope. Sense the  laser supply in parallel as ch1, photodiode as ch2 and compare the on/off edges while driving the laser with a square wave over different frequencies.

1,200 bps is quite slow, but I can imagine receiver clocking problems if the ramp up/down times are not symmetric within say 20%. The photo diode response time will be absolutely fine however.