You have it backward. You don't need to disable some template filter. You need to create and then enable an appropriate template filter.

Your templated javascript contains lines like:

   var test='<%passtoserver%>';
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If the value provided for 'passtoserver' was "Don't do this", then the javascript generated by your template would be:

   var test='Don't do this';
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That is a syntax error. So you need to change your template to contain lines more like:

   var test='<% passtoserver | js_str %>';
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or, perhaps even better:

   var test=<% passtoserver | js_str %>;
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where the "| js_str" tells the template to properly escape any characters that need to be escaped in order to be included verbatim inside of a javascript string literal (and, in the second case, also adds the enclosing quote marks).

And, no, Template::Toolkit doesn't come with a pre-built js_str filter so you'll have to create that as well.

Your problem case is due to the \ character not being escaped for similar reasons. So your template produces javascript code like:

   var test='­[{"name":"­test","pro­blem":"her­e is the problem \" com
+ma "}]';
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And, in javascript, '\"' is the same value as '"'.