This means that the rebel MLAs, if disqualified, cannot be given ministries in case the BJP manages to form the next government following a trust vote.
The Congress and JD(S) are working under the assumption that the BJP has promised ministerial berths to these MLAs. They are using this clause to dissuade the MLAs from resigning, claiming that there is no guarantee that the BJP would keep such a promise once they are in power. And if the MLAs do decide not to come back to the Congress-JD(S) fold, this would be their punishment.
However, there is a precedent that the Congress-JD(S) needs to keep in mind. In 2015, Kerala Congress (M) MLA PC George was disqualified by the Assembly Speaker for anti-party activities under the Tenth Schedule of the Constitution. However, in 2016, Kerala High Court quashed this disqualification and said that when PC George had already submitted his resignation, the Speaker should have accepted that instead of disqualifying him.
Congress Has a Game Plan in Karnataka: But Will It Work? – The Quint