Avoid using Many to Many Relationship
Your 2 table design approach can be implemented using a view. This would not compromise your underlying database design based on 3 tables. 

Views are under used but often give the best of all worlds.

Expanded:

From your "normalised" 3 table design, which looks OK, you will CREATE VIEW (SELECT Employee ID, Language Name, Proficiency FROM Employee, Languages, Employee_Languages WHERE etc. ). Your application then selects from the view.