I've split up my iPhoto library and now I want to clean up (as iPhot crashes around every 5 minutes and I suspect that's due to too many photos in the library).
crashes are rarely caused by too many photos - I have never seen that happen, unless your hard drive has not enough space left for the operating system to work.
The usual causes for crashes are rather inconsistencies in your iPhoto library, importing unreadable or incompatible media (videos, photos), installing incompatible software.
So you'd better find out, what is causing the crashes in this case. Did you install new software, before the trouble started? Or import new photos or videos? Move your iPhoto library to a different location? Run "CleanMyMac" or something similar?
But to answer your question:
Therefore, I want to delete photos from the default library. Of course, I do get a security pop up that reminds me some of my photos have been uploaded to flickr and that these will be deleted as well when I delete the photo from my library.
Is there any way to avoid this?
Sign out of your Flickr account in iPhoto's preferences, before you delete the photos from your main library. Then the uploaded Flickr albums should be safe.
Select your Flickr account and press the minus sign to disable it.