I am a non-resident alien. I discovered that my tax preparer have filed 1040 instead of 1040NR-EZ. I let them know and they said they will be working on it.
A few thinks I noticed.
1. They were standing like they didn't know the details about how to determine whether person is resident or not.
2. They didn't seem happy with my discovery and "kind of" attempted to persuade that IRS will never discover it.

I was wondering what are possible complications may arise with our relationship.
I realize that my amendment may trigger IRS to go over their other filed taxes and they may end up badly.

Is it possible that they may end up paying huge penalties or go to jail? In this case will they try to persuade you not to file amendment? (or in worst case scenario can they even threaten you?)

How can I protect my interest?

Relax, you will not go to jail or pay huge penalties.
Which visa do you have? When did you enter the U.S. Which form/forms did you file in the previous years?

I have F-1 Visa. Entered in the US in 2008. Last two years I submitted 1040's and need to amend them.
I meant punishment for tax preparesrs...

For your tax return, you are responsible to IRS. So if you filed incorrect tax returns, file amended tax returns with properly done nonresident tax returns and Form 8843.
You have to yourself settle with the tax preparer.