The Jekyll documentation says you can use the Jekyll environment to conditionally include code when building the site. For your case:
...
{% if jekyll.environment == "production" %}
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.6.4/angular.min.js"></script>
{% else %}
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.6.4/angular.js"></script>
{% endif %}
...
Another option suggests using another config file specifically for development.
_config.yml sets environment: prod.
_config_dev.yml sets environment: dev.
Running jekyll build --config _config.yml,_config_dev.yml in development, the second config file overrides the first and sets the environment to dev. GitHub Pages runs jekyll build - which only uses _config.yml - and would have environment set to prod. You could use a similar syntax to the above to conditionally include the file.
...
{% if site.environment == "prod" %}
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.6.4/angular.min.js"></script>
{% else %}
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.6.4/angular.js"></script>
{% endif %}
...
