Frank,
I share your concern about the council taking liberties with private land; the fact that the liberty at issue is a tree does not detract from the principle.
You have telephoned them. Why do you not now write to them enclosing a copy of the certificate to which you refer, and a plan showing the length of your front garden and the position of the tree within it? Point out that the longer they leave it in the wrong place, the harder, and hence the more costly, it will be to move, and the greater the potential damage to the tree which they could plant elsewhere. Enclose a photograph if you can.
You could go on to say that if it is not removed within, say a month, you will have it removed by professionals and delivered to their Parks Dept. and send them the bill, which, if is not settled, you will pursue in the Small Claims Court. Copy the letter to your ward councillor, and if you are feeling in a campaigning mood, to the local press.
But you must stay calm and reasonable and not threaten unrealistic rentals.
[Incidentally, I originally typed "yelephoned" at the start of the second paragraph: possibly a freudian slip, but the word does seem appropriate to certain types of phone call.]