Getting into PhD programme when having not the best grades due to personal issues
In Germany even some renowned research institutes mention in the job offers that people with at least grade B should be encouraged to apply for a position. So I don't see here a major problem for you. No one looks on your pre-diploma grades, this is now different with the bachelor AND master degree. But you have to make a presentation of your diploma work for the job interview. I don't know what speaks against adding results that you worked out after that thesis to make the work more impressive, as you didn't have as much time as other students with a scholarship or rich parents and were forced to work besides your diploma work, especially as the diploma needs 12 months in germany. If they want you to send them your diplom pdf, than of course you have to look for another group.

The major problem I see is that you wrote your thesis now 3 years ago, and 2-2.5 years is also a deadline I saw several times in such german PhD job offers, as after some time you simply loose knowledge. 

Nonetheless you should try it, write a few dozen applications and look how much invitations for a job interview you get and in what fields, but be clear what your motivation is. Your question does sound to me like you a bored and desperated in your current job, that is not the best reason for a Prof. to hire you, you should show interest in a specific topic, related to your diploma work would make your motivation to do a PhD more credible to me.