look at this.... although this only reads, I'm sure there is a registry method to write to the registry as well. I would take a backup of the registry before I'd go poking my fingers around in there as well as make sure I'd do this in a sandbox area too.

http://www.databasejournal.com/features/mssql/article.php/3764516

[EDIT]

upon further digging...here is a script fragment...

$protocolproperty=Get-WmiObject -namespace root\Microsoft\SqlServer\ComputerManagement -class ClientNetworkProtocolProperty `

-filter "PropertyName='Default Port'"

$protocolproperty.SetNumericalValue(7001)

this came from the same site I mentioned above but different article...

http://www.databasejournal.com/features/mssql/article.php/3709441