That depends on the javascript code, what it is doing and whether the settings of the page are overruled by http-header.
You could firstly examine whether your webpart uses css-classes. If there is a reference to a css-file in the js-file you could try to change charset property there. Closer to a solution using the same encoding everywhere is of course to save the given files with the expected encoding as described in this post
An overview about the different steps and their effects is given in this post.
And if really nothing else helps than having a workaround setting the output by js than you could manipulate the output by a regex replacing those letters with hex code like in this post