Would you like a PowerShell solution for your query? Once you deploy your wsp package you can run a Tiding up PowerShell script which can take care of all such requirements. Make a PowerShell script file, and write all the functional logic which you want to achieve on top of wsp package. Removing content type can be one of it.
Below is a server side PowerShell script which will remove ITEM content type from the list
$web = Get-SPWeb "UrlOfYourSite"
$list = $web.Lists["YourListName"]
$ctToRemove = $list.ContentTypes["Item"]
Write-Host "Removing Item content type"
Write-Host "Item content type do not exists in list"