One way to get around some of it, is to use WP as a data store and management layer, with your own 2nd layer on top of it, that does use WP's functions to pull that data out, but is not a theme that has to be installed nor activated.
Which is a actually what I've done with my website - but that's not why... It's basically a mini-cms that first checks the file system for the page, and if not found, calls into wordpress.