Developer signed an app with his personal keystore but it should have been the company's keystore.
Is it possible to update the app in the marketplace using the company's keystore now, and still having streamlined updates to users? Are there any consequences of this?
No, you will have to publish the app as a new app in the market. This time signed with the company's key. You will also have to change the package name as it is already used by the app which is already in the store.
When you try to update a app with a version that was signed with a different key Android will show an error to the user telling that the signature doesn't validate.