I am seeking some independent advice to steer me in the right direction. I'm more concerned about long term rusting of a to-be-fixed rocker panel. Let me explain.

Synopsis of my post: (1) which rocker panel replacement method should I choose? and (2) what precautions should I take to keep to minimize the internal rust in latter years?

I have a fairly new car (unibody) for which 30" of the underside of a rocker panel has been gashed out, as if you took a 1" wide finger and removed the metal like butter. Pictures don't do the basic situation justice so I'll leave them out. There's a 12" wide fair depression/bump (but not overly deep) of the rocker panel (as viewed from the side) with the gash starting from the lower-front of the depression and then moving downwards under the rocker panel towards the back of the car. Fortunately the door did not get hit nor deformed. There is adequate and good "pick up" metal on both sides of the gash. It's sort of centered on the door post between the two doors.

My quoted choices of repair have been:

1) Replace with a brand new rocker panel (basically wheelwell to wheelwell) (~$4000)
2) Replace half with new rocker panel (in depressed area) and half with tack-on welded metal sheet (~$2500)
3) Cut out and tack-weld with junk yard rocker panel (~$1500)
4) Tack-weld with formed sheet metal (~$800 - $1000)

The autobody shops which mentioned "replacement" are probably due to the fair (but not too deep) dent in the rocker panel. My preferences are either #3 or #4 (cost wise) and hence why I am penning this forum posting; I am not overly concerned about getting rid of the dent rather than the gash for rusting reasons.

My #1 concern is long term rust inside the repaired rocker panel. I've been dealing with cars for 40 years and know that a car can last forever if there is no lingering rust but even a small pinprick of rust will spread like cancer. The gash has been open to the elements for a while so rust has probably started around the exposed metal.

So my questions are:

1) Should I prefer a simple tack-weld of some sheet metal or replacement with a junk yard rocker panel, given the dent + gash? Again, my concern is long term rust prevention and not so much cosmetics.

1b) How critical should I be, or could I be, with the autobody shop to clean out the rust from the gash + optional junk yard rocker panel replacement before tack welding? Rust is rust...

2) My real concern is long term rust inside the panel. I'd like the car to last another 15+ years. I was thinking POR15 or a galvanic rust inhibitor on the inside of the gash + the optional junk yard replacement. I'd do that myself if I was doing the autobody work but I'm not sure whether an autobody shop would have any interest in cleaning up the inside rust + putting on a rust inhibitor which I were to provide them (or whether they would allow me to come in and apply it myself). In prior situations I did the autobody work myself but this one is a bit beyond my skills.

Thanks for any suggestions before I go and pull the trigger on a shop doing the work for me.

I believe you will have a hard time getting any autobody shop to do a proper rust prevention job on your car. Most are not used to doing this, as it adds hours to a job.
As for the repair, full rocker is always the best bet. It will be just as the factory intended. Strength and durability. Doing any kind of patch work, on a boxed structure like a rocker, you cannot hammer and dolly the welds to get a smoother surface, with less filler. And, by the way, tack welding is not a good idea. Full weld seams are going to hold up much longer, without any filler bubbling up from rust.
As for rust prevention, IF you can get the body shop to make sure all inside surfaces are clean from rust, and treat the bare metal parts, including the areas to be welded,, with a weld though primer, before starting, it's a start. If you are that concerned, I would also have holes drilled in the inner rocker, which later can be closed with rubber plugs, and have a rust preventative solution spraying inside the box structure. There are a few good products for this purpose. While I like using POR-15 for this, it probably wouldn't work in your application, as it works best when applied to bare metal, with a good 2 coats. Hard to do in an enclosed space. And most likely the insides of your car probably has some sort of coating on it already.

Agree with chopolds on the rust prevention measures.

One other thing that you may need to consider is that in many late model cars the sill is an essential structural component made using special steels. Most of these can't be welded or repaired since that would change their strength and therefore must, if damaged, be replaced.

I know it's a confrontational statement but consider the situation if the car happened to get T-boned at some point in the future and the occupant was killed or severely injured when that critical component failed because it wasn't repaired properly, whether or not it looked good and had no rust. Would you be appeased by taking the position "but I saved $2000 in the repair"?