A HCSL clock can be applied at IN2, IN1, or IN0 of Si5341. Regarding to the termination, just use an AC blocking cap in series with each input. This is present a high impedance to the PCB trace and should be what the customer needs since they have source side impedance matching. You can remove the 100 Ohm resistor between IN+ and IN- if the source is terminated properly.
Or you can put the 100 Ohm resistor on the other side of the AC coupling caps but keep the 100 Ohm resistor within 5 mm of the input pins.