It can't be done without calling the "moveFileEx()" API, as WinLogon is one of those files that's executed right at the beginning of the startup sequence. The only real way to call said API is through programming or scripting in a high level language - and even that might not be called early enough.
It's not a program as such though. It's a simple command line utility of the type that can be found natively in the windows and system32 folders anyway. Really, it won't get any simpler, easier, or closer to "not using a program" than that - a short little 3KB script in assembler, aessmbled into an executable single purpose utility.
If you wanted to, you could take the assembler code, assemble it yourself with the assembler it was written for, and then use it, upon which time, appart from the assembler programming, you could say you'd done it from scratch. Even batch files use such programs as the one I gave you - they come pre-installed in XP.
I can think of better experiments than deleting winlogon.exe though.