Whoa... maybe I'm reading too much into the tone here, but it sounds like a chill pill script needs to be administered.
I'm sorry if I came off a bit harsh there - but its a pet peeve of mine that people optimize chars beyond what makes sense from a roleplaying perspective - it was not directed at you (although I can understand if it seemed like it) but more against the principle that I think the roleplaying part of making a character is often overlooked in favor of maxing out game technical capabilities.
A) It's a game
Yes, but its also a roleplaying game - while playing, the player is supposed to take on the role of the character - and as such, it needs to be believable more than optimized

If every character in books, movies and plays where optimized it would truly be some sad fiction

B) There's every chance a PC's development didn't ALLOW for refusal. If an adept works for Aztech/UCAS/Renraku etc, is he really going to say 'No' when the bosses come by to explain a little upgrade?
No, but again, I don't think people (or corps) gamble with peoples awakened abilities like that - they don't have a 0 to 6 rating judging how much bio/cyberware someone can take before being burned out - its a gamble if that piece of "upgrade" will render them mundane forever. Awakened people are damn rare in the world, if a corp (or army) "aquires" such talent, I don't think they are prone to gamble it all for a little cyber/bioware.
C) As for min/maxing, I'll admit this is always a concern. However until the balance shifts back from Bioware towards Magic for what adepts can do, I'll take an R4 Muscle Toner vs 6 points of magic raising my Agilityx4 (@1.5 per point over Racial Limit), thank you very much indeed.
Muscle Toner is ridiculously overpowered compared to everything else - granted, but anyway, my concern is - you should not need to make this choice, yes it makes you better in combat, but if this is a must in campaigns, then we have reached a sad point in the world of shadowrun if it is something everyone just have to have to be able to play. Something I could rant about for a long time in general, any character without extra IP's is basically out of luck in shadowrun these days, the old non-enhanced detective of shadowrun 1st ed is never a viable option if there is just one person in the group going the route of "how do I max out my character", as soon as one person does it, everyone needs to do it at the table to survive the increased challenges the GM has to come up with (which again leads to another series of problems as the GM is then forced to have every single grunt security guard enhanced (or have 30 guards for every runner) - it just leads to a never ending escalation of things.
D) Idealistic PC's while great Roleplaying points, have to accept some limitations in that regard. This is why ideals such as Pacifism or Code of Honour are Negative Qualities in the game. I love them, and they provide fantastic storylines, but they come with a downside, and that can be either external interference, moral conflict, or in the case of outr Adept, falling behind the SOTA curve (which is a MASSIVE downside to magic in general, but that's another thread)
E) there are excellent (and canon) short stories describing Awakened characters accepting Cyber (normally in response to fear from a run that sent them to hospital, killed an ally, or blew off an arm etc etc). This can be just as much of a roleplaying point as the idealistic refusal to accept it.
I'm not saying it shouldn't happen, I'm saying it shouldn't (as it is currently) be the rule, but rather the exception. It should be something done to survive, a whole character concept introduced (hacker adepts as we are originally discussing here

) relying on awakened people with cyberware makes this the rule and not the exception.
F) Shadowrun is about living on the edge, survival of the fittest. Everyone in the Shadows is hunting down the next thing that will help them get more nuyen, survive another day, and maybe, just maybe, give them that big break freeing them from the shadows forever. Sure, some nice comfortable, SINner Magician College professor can afford to maintain his awakened purity, but working in the shadows is not that easy, and any runner (Awakened or not) should grasp any edge that they can get.
And Magic IS the edge - the pure power of it overshadows anything else, and its rare, adepts turning to bio/cyberware is not about the shadowrun universe, its not done with basis in the canon, but with basis in rules and how to optimize your character. The problem may lie in the fact that a pure adept starts the game less powerful than a full blown cyber monster, but in the long run the roles are changed, I think this is the problem - if you had 3-4 more power points from start, I doubt we would see people doing this. Fact is, awakened characters are weaker to begin with, but can advance far beyond mundanes, its a balance problem started with the initiation procedure for awakened. If I could ask for one new thing in Shadowrun 5th edition it would be an "initiation process" for mundanes to remove this problem.
G) By your rationale, there's no market for 2nd hand ware either, as the street sam wouldn't consider such a thing. However, you take what you can get.... This is true even for the awakened...
Not quite the same - a street sam doesn't throw away special abilities, a way of living and seeing life - by using 2nd hand ware, he just gets a bad quality product of what he would have liked to have, a lesser version, lower rating, but still essentially the same he is used to and wants.