The one-time Cabinet minister had the whip withdrawn after voting against the Government on Tuesday evening.
Mr Stewart said the decision on who should be a Tory candidate should rest with local associations.
"This really should be a choice for local Conservative associations and not a central decision," said the former leadership hopeful.
"This is not a Conservative way of behaving."
Mr Stewart is one of 21 Conservative MPs who have had the party whip removed after taking part in a rebellion over no-deal Brexit which will see the Commons take control of the parliamentary agenda.
Others where informed by telephone or in person, while leaked screenshots appeared to show administrators of a WhatsApp group for Conservative MPs urging recently sacked colleagues to remove themselves from the chat.
Some, including former Chancellor Philip Hammond, have suggested that they will try and fight their seats as Conservatives with the consent of local members, with Mr Hammond warning he could take legal action against the national party.
There remains significant unease even among non-rebels about the hard-line stance taken by Boris Johnson against the MPs who voted with the opposition in a dramatic vote late on Tuesday evening.
Sir Roger Gale, who voted with the Government, said the strategy was the work of controversial adviser Dominic Cummings, whom he described as an 'unelected, foul-mouthed, oaf - who should be frogmarched from Downing Street.'
Another series of drama in the House of Commons beckons today, with Boris Johnson facing his first Prime Minister's Questions before a vote on ruling out no-deal on October 31 takes place.
Mr Johnson said he would table a motion calling for an early election to break the parliamentary impasse, but opposition politicians have suggested that they will not vote for a general election until it is guaranteed the UK wouldn't crash out of the EU without a deal by the end of next month.