Logic Circuit Transistor Resistor Values?
The obvious answer is to reduce the value of your pullup resistors (R7 and R8) until the leakage current through the switches produces less than 0.6V of drop.

Anything less than 1 M&Omega; &times; 0.6 / 12 = 50 k&Omega; should work; use 33 k&Omega; or 22 k&Omega; for some extra margin.

You should reduce the series resistors (R5 and R6) to similar values.

BTW, it's R9 that regulates the current through the LED; the other resistors should have no effect on that.