Updating app that has newer version than the store it was bought in
No, you can't update it from Google Play. It would be like buying your phone from Carphone Warehouse and then expecting Phones4u to help you out with a problem just because they sell the same phone. Or buying a music download in Google Play and expecting to be able to download it from iTunes. You've paid Samsung for the app, not Google.

If you uninstall it via the button in Google Play, the app will just uninstall in the usual way. You'll be able to reinstall it from the Samsung App Store if you change your mind, but you still won't be able to download it from Google Play unless you buy it there.

Just wait a week or two to see if there's an update. Apps uploaded to Samsung's App Store have to be "certified", just like Apple's, so there is often a delay before a new version will appear there.