Hi Sandy 791,
From your description, you want to disable Office Web Apps 2013 to specific web applications only.
You can not disable it for one web application. However you can program using PowerShell to disable it for each site collection in a specific web application and this has to be done each time when you add a site collection.
To deactivate the Office Web Apps Feature on a single site collection by using Windows PowerShell:
$webAppsFeatureId = $(Get-SPFeature -limit all | where {$_.displayname -eq "OfficeWebApps"}).Id
$singleSiteCollection = Get-SPSite -Identity http://<site_name>
Disable-SPFeature $webAppsFeatureId -Url $singleSiteCollection.URL
https://technet.microsoft.com/en-us/library/ee837418(v=office.14).aspx#bkmk_deactiv_single
Besides, similar issue post for your reference:
https://social.technet.microsoft.com/Forums/office/en-US/ae95eff5-93d2-450b-bb21-5ba1aef73535/disable-office-web-apps-on-web-application?forum=sharepointadmin
Best Regards,
Lisa Chen