Terminating Unused RF
You will always have some way, appropriate to the level you are working on, to attach a 50ohm load to a port. If it's microstrip, then you'd use a 50 ohm resistor to ground, though two 100 ohm resistors in parallel often perform a little better, and will work for coplanar line as well. 

However, if you have multiple synthesisers and sensitive receivers, crosstalk at RF is too easy to get and too hard to eliminate, that you probably don't want to be thinking about terminating an active output, but disabling it at the chip level. 

It sounds like you're using a dual synthesiser chip and need only one output, but you don't say. Some designs of these will let you switch off the cahnnel or at least the output, for some the best you can do is turn the level right down. For others, programming the output frequency on that port to the minimum possible would make it easier to keep it in its cage.