if you have the icloud account ID and password, you can remove the icloud account on the phone or on-line at appleid.apple.com or www.icloud.com.
if you don't have the account ID and password, you need to either get it from the seller or have them use the websites to remove the account from the phone - presuming the seller is the icloud account owner.
even if this is not the case (seller != owner) doesn't necessarily mean that the phone is stolen or is/will be blacklisted. there are a lot of legit scenarios where a phone is sold with an icloud account that hasn't been removed (ebay is full of them).
however, the bottom line is if you are not able to get the icloud account removed (and it can only be done by providing the correct account credentials - anything you see for services or bypass software do not remove the icloud-to-phone association from Apple's servers, it's just a temporary work around that has to be refreshed/renewed if you ever restart the phone or upgrade the IOS) the you are pretty much SOL.
that said, swapping out the motherboard will require that you change the home button as well (the one matched to the motherboard you're installing), however, changing out the motherboard is essentially the same as throwing away the old phone and using the phone that the new motherboard came out of. everything that apple or the cellular carrier uses to identify a given phone (IMEI/ESN/MEID/etc) lives on and is associated with the motherboard. the "phone" is just the motherboard, all the other components (display, case, camera, speaker, battery, etc.) have nothing to do with the electronic identity of the phone.
let's say you take a motherboard out of a different phone (phone B) and you put it into the phone you just bought (phone A) - presuming that phone B does not have an icloud account on it and has a clean carrier status. activating phone B and putting the B motherboard into the A phone and activating it is exactly the same thing as far as Apple (and the network carrier) is concerned. there is no way that Apple (or carrier) can know that the B motherboard is still in the B phone frame/case OR that the B motherboard has been swapped into to the A phone frame/case. so, no, swapping motherboards will not result in your phone getting blacklisted. blacklisting can happen for a number of reasons, but moving phone parts around is not one of them.
one bright side is that a locked motherboard that can boot up, along with it's matched home button, can have some value by selling it on ebay.
do what you can to see if you can get the icloud account removed by the account owner, but failing that, you're phone (at least the motherboard) is useless. the rest of the phone (display, case, battery, camera, parts, etc) can be used with a good motherboard or can be sold for parts.
good luck to you