Unfortunately it is possible to brick LSI cards by improper flashing, and since it's on the motherboard, that might be a major pain to fix.
The manual for your board should be here:
https://www.supermicro.com/manuals/motherboard/C606_602/MNL-1333.pdf
I would see if you can do any of these, with the SAS card re-enabled:
Try switching between EFI and Legacy mode boot ROMs. I've seen some cards that hang in EFI mode but boot perfectly fine in Legacy mode, or vise-versa. I think this is on pg. 4-16 of your manual, but I'm not positive this setting will effect the SAS card. If this works, the SAS controller might just work fine without re-flashing it again.
If the above doesn't work, try this:
Disable the "Load Onboard SAS Option ROM" and/or "Interrupt 19 Capture" settings. These are on pg. 4-17 and 4-5 respectively. This may allow the card to be enabled but the pre-boot process to be skipped completely. Then, hopefully you will be able to boot your OS and re-flash the card if it's still recognized by the OS.
I also found this forum post about recovering an LSI 2208 which I believe is the same as yours:
I hope you can get it fixed, best of luck.