How to get rid of raw onion smell while doing Gojju when forgotten to fry the onions

Adding fried shallots or caramelized onion may help.

In my experience, a combination of acid (lemon juice/tomatoes/tamarind paste) and heat(temperature) is used to cut the taste of raw onions. You will need to continue frying the raw onion and masala mixture until it separates from the oil, which is a good indicator of the doneness of the onions as well as the spices.
If you follow this route of cooking the onions after pureeing them, you would also not want to roast the spices before grinding them, and instead fry them all together at this stage.