I want to know if we can prevent a Marketo pop-up form on our website from popping up if lead is already in our database?
Yes, and I think this was discussed in another thread very recently.
Enable Known Visitor HTML ("If Known Visitor, show Custom HTML" in Form Editor » Setup) and then have your KV HTML just contain a single hidden tag, like
<input type="hidden" name="knownVisitor" value="true">
Then, in a MktoForms2.whenReady listener, check to see if that hidden field exists in the <form>. If it currently exists, don't show the modal. Otherwise, initialize the modal. Note you can actually use any element, it doesn't have to be an <input>, just something identifiable and unique.