Hi Michelle,
I think what the EK book is referring to is the fact that in forming a peptide bond, the oxygen partially attracts the electron pair of nitrogen to help create a partial double bond, which (in combination with the 3 other single bonds), makes the overall nitrogen structure very stable. You're right, in general, having a tetrameric bonding pattern is not ideal for nitrogen due to the partial positive charge imparted, but in this specific example of peptide bond formation, it is actually advantageous.
Enjoy the rest of the course!