Yeah, I wouldn't ever advise having a BOD of less than 3, but then again I come from a table where there's a 95% chance of at least some combat every session. Even if it's just an unexpected bar-fight or a burglar in your pad, you can't always keep yourself out of the way of danger (especially if you have a BOD of 1, it's your GMs job to bring it to you and make sure you know WHY a 1 BOD is a weakness). Weaknesses are meant to be weaknesses and a 1 BOD is a MASSIVE weakness.
On the same note, I'd probably never have a reaction of less than 3 either - even if you're not combat focused, getting caught with your pants around your ankles will just make it infinitely worse. 1 STR you can deal with (especially if you slap on a couple levels of muscle augs), otherwise just pray you don't ever have to drag your teammate's unconscious body out of the line of fire. IMHO, agility - even for a non-combat oriented character - is one of the most important attributes in the game (again I come from what might be a combat heavy table), because even if you don't need a decent AGI for being the truest of shots, you will probably then want it to keep yourself hidden or use other discreet actions, etc. when the lead starts to fly. If you're trying to squeeze points out of attribute allocation, maybe drop LOG by 1 unless you have some plans for utilizing it? I'm not a fan of investing a lot in EDG, so this would also be a good spot to save BP, IMO.
Regarding skills, I wholeheartedly second Glyph's recommendations. Influence Group, Pistols (they're discreet), Dodge, Perception and Stealth skills. A stealth skill-set doesn't seem contradictory to your concept to me. If one loses their traditional tools of power, ya gotta do what you can, and the easiest place to start could very well be from a covert approach. Knowledge skills should pick themselves for you, Business/Corporate skills/knowledge, Languages, etc.
Regarding Qualities, Double Jointed is a pretty niche application and I wouldn't advise it, also I think you're missing out on some NQs that can provide hooks that are custom made for backgrounds like yours, with the whole "lost glory" and "driven to reclaim it" background. If you know you aren't going to take any cyberware, Sensitive System is great (like if you're gonna be a Adept), but if you're not gonna be an Adept you may want to ditch that - as 'ware is key for a mundane. Some recommended bioware for if you are an Adept and keep Sensitive System would be Tailored Pheromones and Muscle Toner. Other gear to save up for; get tricked out Vision Enhancement contacts and glasses, and Audio Enhancement earbuds. Armor will depend on where your BOD ends up.
Edit: Guess I was typing too slow on this one, 7 ninjas! Dang.