deno run fail to execute npm binary file in 2.0

[avallete]

Describe the bug
Hi there, Andrew from supabase, we've been having report of users failing to use supabase CLI with Deno 2 and running into some error executing the compiled binary.

To Reproduce
Steps to reproduce the behavior:

1. Have Deno 2 installed
2. Create a new directory, and run deno init in it
3. The following content been added to deno.json

{
  # install deps in a node_modules directory 
  "nodeModulesDir": "auto",
  "imports": {
    "supabase": "npm:supabase@^1.223.10"
  }
}

4. Install deps: deno install --allow-scripts
5. Try run the CLI with deno run -A npm:supabase --help

Sees the following error in terminal:

❯ deno run -A npm:supabase --help
error: Uncaught SyntaxError: Invalid or unexpected token
    at <anonymous> (file:///Users/folder/node_modules/.deno/supabase@1.219.2/node_modules/supabase/bin/supabase:1:1)

Debug:

Running /Users/folder/node_modules/.deno/supabase@1.219.2/node_modules/supabase/bin/supabase properly execute the binary.

Expected behavior
Deno 2 with deno run command should also be able to run the supabase CLI

Additional context
Opening the issue based on discussion with @bartlomieju on discord: https://discord.com/channels/684898665143206084/1308818534809210930/1309145748264325120

Related: supabase/cli#2900

Version: Deno 2.0.6