My former boss made an agreement to not involve the cops if I paid the money back and gave everything back. Can I still be arrested?

Yes.  The government, which would be prosecuting you, made no agreement not to.  However, depending on the circumstances (i.e. the amount of money involved, your record, etc.) and the fact that you paid the money back, there's a good chance that teh government won't want to prosecute, or if it does and you are convicted (difficult if your employer keeps his word and doesn't cooperate), may get a minimal sentence.  If your bosskeeps his/her word, the government may never hear about it.