The solution is very simple! And I know because I have the same issues when typesetting Hebrew text. I’m not sure if this works in the regular version of InDesign or only in the Middle Eastern version, but I believe you have the ME version anyway.
Create a character style with only one attribute applied: Go into the character style settings, then into the ‘Middle Eastern Character Format’ pane, and set up ‘Character Direction’ to ‘Left-to-Right’. Save the style, and name it anything you like such as ‘Left-to-Right’ etc.
Then go into the settings of your paragraph style and create a new GREP style. In the ‘Apply Style’ pane select your ‘Right-to-Left’ character style that you just created, and the ‘To Text’ pane leave at the default of ‘\d+’ (which means: ‘any digit one or more times’).
Save the paragraph style, and that’s it! The numbers should be fixed now without having to actually change the numbers which is definitely a bad idea!