The problem is that currently when a player is autofilled he is still matched as if he was on his best role.
The new matchmaking algorithm will be much more complicated because it has to simultaneously look at multiple MMR brackets. Suppose I'm a Plat 3 top laner and a Gold 3 support. I'm not sure exactly how the new system will work, but it has to be looking at potentially putting me in a Plat 3 MMR game or a Gold 3 MMR game (not to mention possible autofill games). (Note: Perhaps for my secondary it will look for Gold 1 MMR games to average out my highest MMR role).
My point is that if you are going to do all this work with the matchmaking algorithm, why not do so but use a hidden MMR for each role rather than having five separate ranked ladders to climb (one for each role)? This would solve the autofill in the exact same manner but would allow players to maintain a singular rank and have every game's outcome go towards one LP value.
For potential abuse, you simply institute the same measures that will be implemented under the new proposed system anyway. For example, if a player queues for an off-role then trades for his main role his LP from a win is significantly less and LP lost is significantly more.