The behavior you describe is exactly how it is intended to work... the script you wrote can only work if it is bounded to a spreadsheet.
The fact that you wrote it in an independent script makes it indeed a standalone app but it can only be executed from within the script editor and in this context an onOpen
function like the one you wrote doesn't make sense (it runs on opening a document/spreadsheet, not the script).
For now a script can only be bounded to a spreadsheet by copy/pasting the code, at least a script that you want to use as you do (with a menu and direct function calls and activeSheet calls), maybe one day Google will expand the concept of libraries to make your script function available from different document directly (read also the doc about libraries).
There are actually 2 types of standalone Apps Scripts, the one you tried that runs only from within the editor and webapps that are deployed and run in a browser window by themselves. The latter are always build around a doGet
function that represents an entry point for the application. You should read the documentation on the subject to get all the details.
To summarize : if you want to access your spreadsheet using getActiveSpreadsheet(
) and similar methods then you have to write (or paste) the script in the script editor bounded to the spreadsheet.
If you want to have a standalone script you can also interact with spreadsheets (and other document as well) but you have to access them by their ID and the spreadsheet will only be viewable from another browser window, without link between them, and there will be no "active spreadsheet" nor "active sheet"...
A webapp can of course also do that with the advantage of a user interface that you can adapt to your needs but this is becoming a bit too far from the scope of your question.
Hoping I've made it (a bit) more clear, at least I tried to make it simple ;-)