Unfortunately this is what I also ran into. Ended up making two separate Photos library - one with about 3,500 photos that is our "system library" and synced through iCloud to all our iOS devices and my wife's iMac, one with my full library (around 75,000 photos) that is not synced.
Only "pain" is that when we take photos with our iPhones, I have to export them from that library and import them into the larger one. And when I take photos with my digital cameras, I have to do the reverse as they are first imported into the larger library.
An option is a program called PowerPhoto (from the Mac App Store) that helps managing multiple libraries - including moving photos from one to the other - among other tools. Tried the demo, but decided that since I really did not need the other tools (though they can be helpful) and I could move the photos back and forth with the import/export steps, the program was not worth the asking price of $25 to me. It might be to you. Several posters here swear by it.