This is a problem. Fundamentally there is nothing you can do - it's just a quirk of OFP, one of many. Sadly there is no "do not fire on tanks, only choppers" command.
The best answer is to redesign your mission slightly so that this does not occur. It is always good practice to create your mission so that it plays to the strengths of OFP, not its weaknesses.
It's not the only answer - there are various heavy handed scripting solutions to this problem which you could apply with varying degrees of success, or rather lack of it. But the plain fact is, if you want to create a really good mission, design around this constraint - don't use scripting to bulldoze it.