configure: improve the prefix warning, and simplify some bits

It's better to compare prefixes than to check if $prefix/bin/mono binary
exists, because in the case of being inside a parallel mono environment[1],
it would warn the user about choosing /usr prefix if mono's prefix inside
this environment is not /usr (i.e.: /opt/mono).

Also, cleanup some variables:
* CANON_MONODIR not needed, as it's actually just Mono's prefix.
* No need to check both Mono's libdir and prefix via pkgconfig, as
these two variables have been both there in Mono's PC file for years [2],
and anyway the existance of $MONODIR/2.0/mscorlib.dll is checked later,
just in case.

[1] http://www.mono-project.com/Parallel_Mono_Environments
[2] https://github.com/mono/mono/commits/master/data/mono.pc.in