You're confused..willfully not using their powers or not using them properly isn't the same as being powerless. I would suggest that the SFA should do everything they can to make sure it doesn't happen again and ensure that they have the cleanest hands in Scotland. Whether they do so is up to them.
What did they have to do with UEFA?
Not really, they can expel clubs if they want. There's lots they can do in the right circumstances, the question is are they willing?
"The authority to impose sanctions is contained in Article 112 of the Scottish FA Articles of Association which states that a club failing to comply with the requirements of National Club Licensing shall be liable to a fine, suspension, expulsion, or a combination of these penalties or such other penalties, sanctions or conditions as is considered appropriate in the circumstances."
There you go.