Tim,
Yes, you can turn off Javascript validation in MyEclipse. Please follow any of the following steps :
1) To disable validation, you should be able to go to Project Properties > MyEclipse > Validation > Excluded Resources and check the tree you wish to exclude.
2) You can right click on the folder or individual JS resource and select MyEclipse -> Exclude from validation.Once you select the Exclude from Validation, you need to make a change and then save the js file to remove the errors. Ex : Hit space and then save it.
3) You can globally disable the javascript validator from Window > Preferences > MyEclipse > Validation. Uncheck both the boxes for ‘JavaScript Validator for JS Files’. This will trigger a full project rebuild, after which, JavaScript validation will be globally disabled. You will need to restart your workspace for it to remove the error markers from files that had already been validated before you turned it off.
Let us know how it works for you.