Hi Prachi Bhalika,
Your case has two dimensions. One is violation of service agreement signed. Second is dishonor of cheque. Employer has all the right to file criminal case.
You should not have left the company without notice period /information. You claim you have been hospitalised which proof you should have submitted with your HR to show your genuineness.
Now better you contact your HR and request for amicable solution. They may initially demand much, but present your case with medical records and try to negotiate for 1 or 2 months salary maximum.
Please don't issue security cheuqe/don't sign service agreement if you are not sure of continuing with any employer. Leaving the legal validity aspect aside, it will be harassment for you as they continue to serve legal notices repeatedly.