In a minority opinion answer to your first question, I would certainly choose a .357 over a .45 ACP–especially with that big Ruger–but only because I am fairly well trained with a revolver and have years of reflexive skills to lean on there, while I consider auto shooting to be a bit more of a commitment.
(This goes triple or quadruple for my .45 of choice–my colt commander. I might be less concerned with my own competence in the middle of the night if I owned less of an "experts" gun, say, a Glock 21 or something...).
In short, I'm basically a revolver guy (on this forum, go figure); especially for HD, FWEIW.
Like highorder alludes, with a 6-inch Ruger, you can pretty much write your own ticket for this type of job. There's a lot of load options out there. Flash with good loads will be greatly reduced in the long tube (perhaps even perfect, just enough to illuminate the sights with low-flash tac loads... you'd have to try some in low light to find out for sure!) and ballistic performance and controllability are both enhanced.
So far as over penetration is concerned, IIRC, the border patrol used 110 gr. loads for some time, in part for concerns of that nature. At the speeds that even the milder 110s will be generating out of that long tube, it's possible that you might actually want more penetration on "active" targets, not less.
I'd personally vote for keeping the GP 100 close at hand with medium velocity tac loads (ie; 125 gr. golden saber Remington, Corbon dpx, Buffalo 125 GDHP lite). I'm no big expert, mind, but I'd think that these would be at max velocity for bullet design out of the 6-inch gun, low flash, lower report/blast (perhaps a secondary but, as mentioned, very real concern for HD) and *especially* super-easy recoil in the big Ruger–by .357 standards.
With a sidearm that size, you can totally have your magnum cake and eat it too, IMHO.
Just one opinion, of course, other equal-to-more qualified opinions may well differ. Beyond that, if all I had was the .45, I'd make do somehow...
