configure: remove --ninja switch

It is unknown if there are any users of the ninja build and keeping it
around makes refactoring the build system more difficult.  It's partly
broken (or at least, deeply inefficient) because it touches out/Makefile
every time.

PR-URL: https://github.com/iojs/io.js/pull/467


Reviewed-By: Chris Dickinson <christopher.s.dickinson@gmail.com>
Reviewed-By: Rod Vagg <rod@vagg.org>