I don't think this is anything to worry about and in fact based on how teleportation machines are likely to work it's not even a threat full stop.
In order to teleport something, you would one way or another measure the "quantum state" of the system, and then transmit that measure elsewhere. This isn't going to be a direct measurement, but would be done using the properties of entanglement. The technical details of how this work don't overly matter for now, but the end result is that the teleportation machine measures something and, critically, what it measures will be radically different for a fly sitting on a human from what it would measure if the fly and human were to merge in some way.
Moreover there is no risk of the information decaying from the one state to the other (or, at least, one can safely assume that this risk is negligible). The result is that if a working teleportation machine were ever built it would almost certainly not lead to such bizarre scenarios as a "super-intelligent virus".
Quite apart from that, the practical chances of building such a machine are vanishingly small, at least for the foreseeable future, so that everyone here will be long gone anyway.