An easy way to fix the mismatch would be to purchase 2 x IOM6's to swap out with the IOM3's - ONTAP will essentially treat it as a DS4246 (even if the HDD's themselves are 3Gb/s SAS.).
If you don't go that path, it's not really a blanket statement that everything is throttled down to 3Gb/s on the stack.
SAS is a point-to-point protocol. The speed of a connection during its duration will depend on the components in the path of the connection.
If the path goes through a IOM3 in the DS4243 shelf or terminates on a 3Gb/s HDD/drive, then the connection for that I/O transaction will run at 3Gb/s.
If the path to a 6Gb/s drive only has 6Gb/s components in it, then the transaction is at 6Gb/s.
Let's assume that you have multi-path HA cabling (MPHA) and you put the DS4243 at one end of the 7-shelf stack.
ONTAP will choose the "shortest path" to the HDD/drive.
This will mean that 4 of the shelves will be accessed from one end of the stack while the other 3 will be access from the other end of the stack (again, assuming you have properly cabled for multipath HA (MPHA).
So, this means that 4 of the 7 shelves will be able to form SAS connections at 6G/bs speeds 100% of the time. The other 3 (including the DS4243) will run with 3Gb/s connections if the path goes through the DS4243 first (at the end of the stack).
Having said all that, I doubt you'll see any tangible performance difference, anyway. Even 3Gb/s SAS is 4 x 3Gb/s lanes = 12Gb/s bandwidth for that path to the 3 shelves from each controller's SAS HBA port.