How do I get around this without deleting the .git/worktrees directory?
You will have an easier time with Git 2.17+ (Q2 2018), since "git worktree" has learned 'move' and 'remove' subcommands.
See commit 7f19def (04 Mar 2018) by Eric Sunshine (sunshineco).
See commit ee6763a, commit cc73385, commit 78d986b, commit c64a8d2, commit 9f792bb, commit 9c620fc (12 Feb 2018), and commit 4ddddc1 (24 Jan 2018) by Nguyễn Thái Ngọc Duy (pclouds).
(Merged by Junio C Hamano -- gitster -- in commit bd0f794, 14 Mar 2018)
In your case, you could move the existing worktree to the place you now wants it (when attempting to create a new worktree for the same branch).
worktree move: new command
This command allows to relocate linked worktrees.
Main worktree cannot (yet) be moved.
And:
worktree move: refuse to move worktrees with submodules
Submodules contains .git files with relative paths.
After a worktree move, these files need to be updated or they may point to nowhere.
This is a bandage patch to make sure "worktree move" don't break
people's worktrees by accident.
When .git file update code is in place, this validate_no_submodules() could be removed.
Note: before Git 2.21 (Q1 2019), "git worktree remove" and "git worktree move" refused to work when there is a submodule involved.
This has been loosened to ignore uninitialized submodules.