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.
Let us know how it works for you.