Disabling the vanilla data pack disables certain game behaviors. This currently includes, amongst others:
- Leaves start decaying
- Anvils can't be opened
- Marking maps with banners won’t work
- Lava same color as water
The issue you are reporting now, which is specific to not loading vanilla datapack, is working as intended. If you do not provide a definition of what lava is, the client will not know and that is undefined behaviour. If you intend to replace vanilla datapack you must make your own definitions of things instead.