It may be a problem with how liquibase tries to break up the SQL statement into separate blocks to feed to the database. Liquibase should just be dividing them up with a line separator regular expression on the GO but if it was dividing it up so the IF is one statement and the inner block is another it may still always evaluate the inside block. If that was the case, though, I would think the IF portion would give a syntax error since it is probably not a full statement.
To be sure, you could use splitStatements: false in your changeSet definition. That will cause liquibase to send the whole string to the database as is.
Nathan