What to reply to your former supervisor that wrote that your paper "isn't worth much" before submission to a journal?
In the last months, I wrote a paper about an aspect of my thesis, with
  the collaboration of my former supervisor.


That means that the paper is not 100% yours. Do not add or remove co-authors on the basis if you like them or hate their guts. 


  Having the paper accepted in this special section may be the best
  thing that could ever happen to our our paper


Sounds like excellent advice. Special issues are more focused, have shorter response rates and usually easier acceptance for more focused papers.


  Writing this request to the editors may cause a lot of problems"


Also excellent advice. You want to contact the editors to do the review of your paper sooner just for you? This is simply stupid.


  should focus on how to improve the paper, instead of inventing new
  ways to create problems


You have four months to improve the paper. Are you sure that it cannot be improved? Are you afraid that your competitors might publish sooner? If yes, submitting to the journal now, will not save you anyway. Could you not upload on arxiv? You should also discuss this with your advisor. 

Conclusively, cool down. As a PHD graduate and not a student anymore, you must behave always as a professional. Perhaps your paper is not that great (perhaps it is). That is not an insult - it is the sincere scientific opinion of one of your more senior peers (who contributed to your success). Do not burn bridges with your supervisor, just because he expressed his honest opinion (even if you do not agree with that).