^^ Fourth'ded... I'm with ZeConster, Crunch, and Mirikon on this one.
Just because you have a Corp SIN doesn't mean the corp has an outstanding bounty on you, at least not according to the text as written.
Given how many people conceivably work for Ares, or S-K, or any other mega, it'd be a logistical nightmare of epic proportions just to keep track of each and every Corp SINer who went AWOL, never mind trying to bring them all back in the fold.
I also find it completely believable that a Corp SINer could be an actual undercover agent for his parent corp, in which case keeping this fact from his compatriots would be even more relevant.
In any case, having to taking reasonable steps to hide ones identity to avoid being shunned, hurt, or worse by ones fellow runners, paying 10% of all income (either back to the corp or as a money laundering "fee", if you will), and having to role play one of the privileged few who grew up with a corp SIN (and who is very likely more than a little brainwashed as a result) and either chose to or had to leave the corp seems fair for the karma cost compared to some of the other negative qualities, at least in my view.
The very real challenge comes in the form of role playing a desire to not run against your parent corp without giving away your secret. How do you explain to your team mates that you don't feel like doing this run because it is against your corp? What happens if you do the run; can you alleviate your conscience by nabbing the pay data and giving it back to the corp with a "this is no longer a secret" flag? Would you write one act off against secretly funneling other info to the parent corp on a regular basis? How do you play a reticence to act against a certain party that is hardly innocent in any way, shape, or form.
As an example, the background for my SRM character is one of a human male in his mid-30s who grew up an Ares SINer in Seattle, joined the UCAS Army and served for about a decade, and who returned to Seattle after receiving an honorable discharge despite rumours of drug use as his Corp SINer parents pulled some strings. Disgruntled with civilians complaining about (in his opinion) trivial matters, he relocated to Chicago when a former team mate set him up with a security contract and he's spent the past five years there, effectively living off the grid (as many real world veterans did and still do when returning from active duty).
While I haven't currently because of SRM potentially being GMed by different people, in a home game I would easily have taken the Prejudice negative quality against the common group Civilians (i.e. all non-military) as a bias, and the mild Cram addiction to further build up the character background with qualities.