Original Certificates and Employment Practices
Keeping original certificates is done by colleges at the time of admission to prevent students from taking admission at multiple colleges. It is strange to be asked for or to have deposited original certificates with a company. For decades, it has been known that what one submits or is asked to submit while applying for a job are attested copies of the certificates, and verification of the same is done at the time of appointment. The person verifying the copies should promptly return the originals. Senior HR Managers from this forum can shed light on this matter for the benefit of non-HR forum members.
Exiting a Job and Employment Bonds
Regarding exiting a job, although I am not from HR, having seen the industry for over 40 years, I can say that no one wants to keep someone in service who is not interested in the job, as they may not be able to put in maximum effort and hence produce results. In the case of senior personnel, even if there is a bond for up to three months, companies do relieve them as quickly as possible with mutual agreement.
In your case, the employer certainly must have a waiting list of other potential candidates when you were selected. Hence, it could be easier for them to fill the vacancy quickly if you leave. Ms. Sharmila Das has indeed given the best advice; talk to the seniors, explain your difficulty, and a mutually agreeable solution may emerge.