configure: fix --enable-check-runtime-deps

Checking runtime deps is the default, but a bug in the configure script
would turn the feature off if --enable-check-runtime-deps was given.

This makes it do the right thing in all five conditions:

(no argument given):             do runtime dependency checks
--enable-check-runtime-deps:     do runtime dependency checks
--enable-check-runtime-deps=yes: do runtime dependency checks
--enable-check-runtime-deps=no:  skip runtime dependency checks
--disable-check-runtime-deps:    skip runtime dependency checks