Normally we limit current to devices that can draw excessive current under some conditions (like LEDs), not to circuits that are handling such loads. In other words, your timer should be robust enough to handle whatever the motor draws, because if you reduce the motor's current, you also will probably reduce its speed, torque or both. So if your transistors can't handle it, then you should get some bigger transistors (current-handling wise).
One thing you should do, since it's a DC motor, is to put a "snubber" diode across it to absorb any reverse inductive "kick" (you'll find tons of info on this by a simple search).