I don't think that I missunterstand the ruling, but here is no "strategy" forum for my topic...
However, reading the Mission Setup, the Imp chooses its open groups (OG) at step 3. and the Rebells may deploy an ally at step 7. Hope this is correct.
The point is, that the Imp maybe choose other open groups, when knowing about the extra threat gained by deploying the ally, but by this ruling the Imp does not have this information. So how do you choose your open groups if the Rebells have, for example, the option to bring Luke Skywalker to a mission?
When having 3 OG, ok you can choose 2 not to expansive groups which are good for your goals and a more expensive group like elite Royal Guards or Darth Vader to "counter" deploying Luke. In most mission you do not loose flexibility or have a big strategic loss, but whats about missions with only 2 OG? Did you prefer a maximum of flexibility or take you the risk of picking a group that you possibly will not be able to deploy unless the ally is deployed?
Hope for a nice discussion, maybe the question cannot answered in general, so feel free to specify your answer to a specific mission.