IMO, a little cyano in your fuge isn't a problem. You have to watch it however, make sure it doesn't get out of hand. Cyano can indeed smother chaeto as it is a far more aggressive grower. Excess cyano may mean you have a nutrient balance issue that your filter isn't addressing.
Also, remember that chaeto is only a moderate nutrient exporter....and that the only way you're really going to "export" those nutrients bound up in the chaeto is by pruning the macroalgae ball and getting rid of portions to allow it to grow back. Caulerpa is known to be a faster and more aggressive nutrient exporter; however, there's a high risk it will go sexual and re-release all those nutrients back in the tank.
I've seen sumps that were crystal clear, and sumps that looked like Swamp Thing's Outhouse. It all boils down to what your display tank looks like....if your DT looks great and your chemistry is in place, then it's up to you to decide if you wish to battle the cyano that may be hiding out in your sump. Good Luck!
