in my opinion taking into consideration above facts the court should not grant injunction.

For an interim relief of injunction, the factors to be seen are:

1. Prima Facie Case

2. Balance of Convenience

3. Who will suffer if the injunction is not granted

i do not think that upon an unregistered sale deed and the case filed beyond 3 years i.e. period of limitation, any ground for injunction is made out.

Your question : "Can any court of law grant injunction of the property whose sale deed is unregistered" is misconceived.

You should be concerned with the order passed in your case and seek opinion from your lawyer about its validity, if you intend challenging the same before higher courts by of a Revision / Appeal or any other remedy available in law.