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
Add-PSSnapin "Microsoft.SharePoint.PowerShell"
$web = Get-SPWeb "UrlOfYourSite"
$list = $web.Lists["YourListName"]
$ctToRemove = $list.ContentTypes["Item"]
if($ctToRemove)
{
Write-Host "Removing Item content type"
$list.ContentTypes.Delete($ctToRemove.Id)
$list.Update()
$Web.Dispose()
}
else
{
Write-Host "Item content type do not exists in list"
}