can we use *since* before *died*?

Yes

Surrender, Singh, an eyewitness who has since died, had claimed that three men were at the spot and were witness to the riot.

Should a comma be inserted after 'Surrender'?

I imagine that Surender Singh is the witness's name.

Does "has long since died" have the same meaning as "died many years ago" ?

Yes

So "since died" means died long ago?

fivejedjonI imagine that Surender Singh is the witness's name.

I see your point.

No

then what does it mean?

Long since means long ago.
Since in a context like the above example means since that time. In this case Singh made the statement, and at some point after that but before now, Singh died. Singh may have died yesterday, we are not told.