It's as if he was preparing to have amnesia. Also, how did the 'surgeon' manage to find it?
I personally think the implant of the laser was to reveal Bourns own identity to himself if any accident happens.
It was likely from the beginning that Bourne may get amnesia due to the drug effect. So if anything of that happens, he can get back his identity easily(Like the movie went on). Maybe they thought, it will create pain in the implanted area and he would eventually find it. But I guess, his employer did not think that after committing to the plan, he would turn against them.
The doctor found the laser because he wanted to examine an severely wounded body thoroughly. So he found the scar, felt something inside it and made it out.
In his line of work it's a lot more likely that he was planning on dying rather than having amnesia someday. The implant was probably intended for his employer's benefit, not his own.
The 'surgeon' found the device when he pressed on the scar and noticed that there was something under the skin. It was a small device, but it would have to be big enough to feel if it contained a working laser and battery. Remember, Bourne had two bullet holes in him at the time, so it stands to reason that he'd get a thorough examination.