Bondo will absorb moisture over time and cause rust.
Welding is extremely expensive and has a good possibility of causing the sheet metal to warp. Additionally, it is very hard to grind to the surface of the surrounding metal.
The way we used to do it in a body shop I worked at years ago, is the same way we used to fill the holes used to pull dents. If there are a lot of them and / or the structural strength of the metal is compromised by the number of holes, either weld or braze.
If on the other hand you are just talking one or two holes or in the case of trim holes, then get yourself a heavy duty soldering iron, the tip kind and some acid core solder and flux. I'm not talking the little soldering iron's that you can do wiring with, or even circuit boards, the iron I'm referring to has a tip about 3/4 to an inch in diameter that tapers down to a tip, either at an angle or like a pencil. It may be rated 100 to 250 watts. Your Grand Dad may have used it to fix old pots and pans with.
The procedure is simple, heat the soldering iron, and while it's getting to temp, with an air grinder, spot the holes you will be filling, then apply the flux. The flux will etch the metal so it will receive the solder uniformly and not bead up. Once the iron is up to temp, touch the tip to the hole, hold it there for a couple seconds, then touch the acid core solder to the tip of the iron closest to the hole. The acid will be close enough to the hole to flow in there and do further etching and the solder should just flow in and fill the hole.
Take care not to overheat the hole or the solder will not stick. If this is the case, go on to the next hole to allow this one to cool down. If you don't touch it or have a lot of junk in it, you should be able to just use the acid core solder and iron to fill. If you have gunk then spot with the air grinder.
I've personally done several cars with this method, it is quick and easily worked. You can usually do a complete side of one car in about 10-15 minutes. The holes are small enough that you haven't compromised the metal by using solder and the solder is very easy to sand / grind down to shape and not require much filling with red cap over it.
One note, make sure you wipe off any flux or acid that may flow down, as it will continue to etch and can cause corrosion. Usually a rag soaked in acrylic thinner will cut both of these.