People need to move house for many reasons, job, health, family, personal circumstances change etc. they should be able to move easily, without a financial penalty being paid to the government. A simple fee to cover the administration cost of registering ownership would be perfectly acceptable.
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Most people add the stamp duty tax to their mortgage. How can taking out a loan for 25-30 years to pay the government for the privilege of moving home be right. Capital gains if it's an investment - fine, Council tax - fine, Tax preventing people moving house, not fine. Stamp duty prevents people downsizing before retirement, and prevents people moving for any one of a number of reasons.