Cyclone V clock pin driver output impedance

When measuring a clock (or any high frequency signal) with a scope, be careful with the ground connection. If your scope probe ground connection is far away from the signal you are measuring, it can appear more distorted than it actually is.

In your case I think a 33 ohm resistor in series, close the the FPGA, will be enough. Yes there will be a reflection when the signals arrives at the ADC, due to the high impedance on the input, but the reflection will just go back towards the FPGA and be absorbed by the serial termination there. As far as the ADC is concerned, the clock signal should look clean.