Learn English – The past perfect without a simple past time clause. “I had eaten the day before.”

A bigger problem with all forms of 2 is that the second comma shouldn't be there.

In "However, they didn't know that Brian had flown to Brazil the week before, and had been abroad when the burglary took place." the comma breaks up the list of things "they" didn't know, which was one intended purpose of the "and". The "and" now makes the "had been abroad..." refer to the "they" instead of "Brian".

The "was abroad when the robbery took place" is a direct consequence of Brian's having gone to Brazil, and is the other purpose of the "and" (i.e. "and therefore").

A sentence shouldn't start with "however", either, so a better construction would be:

"They didn't know, however, that Brian had flown to Brazil the week before and had therefore been abroad when the robbery took place."

In general I agree that using ago implies that the simple past would work better. In this case, however, the simple past doesn't provide the obvious and relevant connection/link between the two sentences that had planned offers.

If it were me, I would use had planned (for its link to the previous sentence) but replace ago with prior to avoid any subtle semantic imperfections. (Edit: Except you stated that the semantic intent was half a year before "now"... So this suggestion is less useful.)

With that said, neither example is particularly offensive, and I doubt that other native English speakers would have strong opinions either way if they encountered either example in real life.