Our checkout combines, and works fine. Been combining for over a year and a half.
There are maybe 20 posts in the checkout forums, and most are questions about it, not problems. We're processing at least a million checkouts a month from a pretty large number of sellers. How does turning it off make things easier for the seller? I can't think of any ways. The only people I see suggesting to turn off the checkout are those that don't use it.
We're a free service but we need things like checkout turn on to keep it that way. What I'd suggest is to leave it on. If it ever becomes a problem turn it on then.
It's better for a seller to process their own checkout. It gives you more power, and eBay less. That is a strong position to be in. Unfortunately eBay knows this so they have stupid rules that do things like ban Google payments. That can't last forever though. Having your own checkout also lets us brand the checkout as you, upsell your items, accept credit cards through your own merchant account if you'd like etc. More power, and more choices for the seller, less for eBay, and that can't be anything but a positive for the seller. Also consider that when we add stores your buyers won't be able to combine purchases from your store and eBay unless you have our checkout enabled.