Another difference is that the countries that refused passage to President Morales didn't lie about a bomb threat. Belarus's actions possibly violate the Convention for the suppression of unlawful acts against the safety of civil aviation. Article 1.1(e) forbids any person from communicating "information which he knows to be false, thereby endangering the safety of an aircraft in flight". Belarus is a party to this treaty. So there need to be serious consequences for what Belarus did on Sunday.
Finally, Belarus's actions wouldn't be justified, even without the false bomb threat, and even based on its authority over its own airspace, which is technically unaffected by the IASTA. Unlike the countries that refused passage to President Morales in 2013, Belarus waited until the RyanAir flight was about 30 minutes from exiting its airspace. Those countries denied passage to President Morales before his flight entered their airspace.
It would be bad enough for a country to give a flight permission to enter its airspace with the intent of revoking that permission before the flight can actually complete its journey over the country. Even if a country does revoke permission of a flight after the flight has already entered its airspace, however, that revocation only means the flight has to leave the country's airspace as quickly as possible. Revoking a flight's permission to be in a country's airspace does not mean that the flight has turn around and land an airport of that country's choosing