IMO There is NO difference in quality between the SA M1A and the Ruger Mini-14. They are both very good quality rifles that are vary reliable. The Mini-14 has been trusted by law enforcement and civilians for years, it is an ultra-reliable and dependable rifle that will not let you down.
I feel the 5.56 is a better round for self defense because it will get the job done and wont pass through a city block of houses before it comes to rest. I for one do not want to kill my neighbors kid after the bullet passes through a bad guy and goes through 2 more houses.
IMO The Mini-14 is just as good as the M1A when quality is concerned. The 308 is not a BETTER round, it is a larger more powerful round that is better for long range kills or shooting through barriers.
My experience leads me to believe you are wrong on all accounts.
The most accurate Mini I've ever seen was a Ranch Rifle my uncle owned. It has a 3-9 scope on it and would do 3 to 4 inches from the bench. It would also ding brass up and throw them 50 feet from the rifle, and would malfunction on a regular basis. My dad has a pre-Ranch that has trouble doing better than 4 inches with anything from iron sights. He's handloaded for that rifle for years but never found a combination that does any better. Meanwhile, I can take cheap 147 gr FMJ from S&B or WWB and easily hold groups of half the size with a bone stock M1A Loaded and iron sights. My M1A has been smoother and much more reliable than any Mini I've ever handled or shot. Heck, I can get Mini-14 accuracy from a Romanian AK I bought new for $279. I have a Yugo SKS that aside from being more reliable than any Mini-14, also groups inside 2 MOA with Wolf ammo.
Likewise, while the .308 is a better round for long range applications as well as for barrier penetration, as stated, it is also capable of being loaded much better for defensive applications. Consider that the 155 gr Hornady TAP displays near perfect penetration for defensive applications while offering cavitation and tissue displacement about 70% of the standard 12 gauge buckshot load. It has less recoil and much greater capacity than any shotgun at much greater terminal effectiveness than any 5.56 load existent. It will be loud, but then, the 5.56 indoors isn't pleasant either.
The only thing the 5.56 does better than the 7.62 is the dedicated varmint rifle, and for that role, the Mini-14 is about the least logical choice that can be made. I am not an AR advocate, far from it in fact, but the AR is the better rifle--much more accurate and probably more reliable than the Mini. The SIG and XCR, the AUG clones, even the AK clones--all of them are likely to be both more reliable and more accurate than a Mini-14. Ruger can give away all the 20 round mags it wants. The simple fact of the matter is that the Mini-14 is a bastard abomination of a rifle that somehow manages to take a platform known for its reliability and accuracy and turn it into a rifle known for its lack of both. So cartridge debate aside, even if the OP decided on a 5.56, the Mini-14 should be on the very bottom of his list.