I'm afraid that it's not that easy. If it were, people would have converted the majority of 400/800 software LONG ago. Heck, somebody might have just written a conversion program to do it automatically. The reason that neither of those are true is because it is NOT that easy to convert a binary to run on a different machine. You can't just delete portions that the 5200 doesn't understand. You need to disassemble the binary, reverse-engineer the program, edit the problem routines, then reassemble into a new binary.
The reason that disassembly is required is because the equates have all been changed between the systems. For example, to set sprite 0 to a horizontal position you'd store a value to a specific memory location...that memory location is incorrect when it's ported to the other system (it uses it's own set of equates). So the entire program needs to be disassembled so that all of the equates can be changed to the proper addresses. For the most part, this IS automatic...there are disassembler programs that can do this automatically given only a few parameters (such as the ORGigin address)...and the 5200 equate table can be pasted right into the disassembly.
Next, reverse-engineering is required to be able to rewrite certian routines by hand that cannot function on the other system. Reverse-engineering is examining and decyphering the program...in order to locate routines that need to be altered (and deeper...any other routines that clash with those). User input is one such example. Ram usage is another. Just as system equates are all different between systems, so is how the platform's operating system handles such things. No point in converting a program if the original expects more ram to be present than the 5200 system has. If that is an aspect, it adds one more headache to the mix...the program will need to be redesigned to work with less.
Once the binary has been disassembled and edited to function on the new system, it can be assembled into the final binary. If everything has been handled correctly, the new binary will be compatable with the intended system.
I dunno what you mean by "start right away". All programs do this. Of course, a broken program that has portions deleted will crash the system...just the same as the unconverted program would. This does not mean that it failed to run right away...just that running right away still left unresolvable problems that the system could not deal with.
In short, you underestimated the scope of such a project. Starting with an unfinished program already places the person doing the conversion at a disadvantage. Since it was never finished, there may be unresolved problems present in the code that never worked correctly on the original system. These glitches will be ported along with the rest of the code unless somebody is very aware of what the program does. As mentioned, it would be better to choose (at least) a finalized program for conversion. Fortunately, there are plenty to choose from. Some of them even have source code available to eliminate steps 1 and 2.
Have you played a Parker Brothers game? Well, what I mean by "start right away" means that when you play a Parker Brothers game, (Pac-Mac is Parker Brothers) you don't see something that says COPYRIGHT 19 ATARI, the game just starts right away. I have been answering questions today too much!