Today, I eventually managed to migrate my entire code from V1 to V2. I had pretty heavy integration with React-Moralis, and the previous database system.
In the process, I removed a lot of dependencies with Moralis codebase and now rely more on Firebase for basic functions and wagmi. This felt good. I think I am definitely more scalable now.
This was a lot of work and took an entire month of my free time.
I am glad to be there and my website is functional again so I should be able to release soon.
If another large deprecation like that would to happen again, I will probably try to remove my dependencies with Moralis codebase. Hopefully v2 will be more stable 
The point with using Moralis initially was to save time and I am not sure this has been my experience due to this deprecation.