Yes, yes you can. Scripted or automated deployment can be done in a number of ways in SQL Server 2012.
Integration Services Deployment Wizard
Yes, this is the primary UI tool for SSIS project deployment, but it can also be run silently on the command line. When you run through the wizard, the Review page will actually list all of the parameters you need to do the same deployment from the command line.
Run ISDeploymentWizard.exe /? from a command prompt, and you’ll see the full list of arguments it supports.
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SSIS Catalog T-SQL API
DECLARE @ProjectBinary as varbinary(max)
DECLARE @operation_id as bigint
Set @ProjectBinary = (SELECT * FROM OPENROWSET(BULK 'MyProj.ispac', SINGLE_BLOB) as BinaryData)
Exec catalog.deploy_project @folder_name = 'MyFolder', @project_name = 'MyProj', @Project_Stream = @ProjectBinary, @operation_id = @operation_id out
All SSIS Catalog operations can be automated through PowerShell. I previously blogged about a deployment script I use to setup my demos.
The SSIS Catalog management object model (MOM) exposes a set of SMO classes you can use to code your own catalog utilities. You’ll want to use the CatalogFolder.DeployProject method to do the actual deployment. If SMO or .NET isn’t your thing, you can also code a custom utility which interacts directly with the T-SQL API.