Preparing for travel with pending EEA(FM) application [closed]

My spouse (US national) and I (German national) have both been living and working in the UK permanently for a number of years. She's currently working here on a Tier 2 visa and I'm exercising treaty rights. After our recent marriage (in the UK) we filed a shared EEA(FM) and EEA(QP) application, which is pending, and will most likely remain that for a prolonged amount of time (judging that it does seemingly take up to 6 months for others).

As part of the EEA(FM) and EEA(QP) applications we submitted the following (original) documents:

• my spouse's US passport
• my spouse's BRP (Biometric Residency Permit for the Tier 2 visa in the UK)
• my German ID card
• our marriage certificate (the handwritten one you get on the day)

Because we knew that we will want to travel we took a few precautions and got my spouse a second US passport from the US embassy. That was a pretty straightforward process as she told them that the UK government will keep her first passport for a prolonged amount of time. We also got an official copy of the marriage certificate and I retained my German passport.

We'll only be traveling to Germany (returning from either Switzerland or France if that makes any difference) and I don't believe there should be any problems to travel there. It'll be only a short trip to Germany over Christmas. She'll just enter the Schengen area as a tourist as she always did, now with her second passport.

The way back to the UK seems slightly more tricky. She'll be able to board the aeroplane as US nationals don't require visas to come to the UK (as tourists) so she'll surely be able to board the plane back. After that we will need to re-enter the UK and usually she presents her passport and BRP and after a few questions, she's back. This time however we won't have the BRP (as it's with the Home Office for the EEA(FM) application).

As far as I understand she has (in theory) three different ways of entering the UK:

1. As a tourist (bad idea I believe).
2. As the spouse of an EEA national (me), travelling together.
3. Under her own Tier 2 visa (lacking the BRP).

I believe entering as a tourist is a really bad idea as that would invalidate her Tier 2 visa that her current job is on. Entering as the spouse of an EEA national might come with the same problems (unsure) and we would probably need to prove our marriage at the border. Our plan was to bring the official marriage certificate copy and a proof of employment from my employer (which should show that I'm a 'qualified person').

The third option is of course for her to enter the UK under her Tier 2 visa, which I believe would be preferable as it clearly can't have any impact on her current job. The issue will be that she won't have a BRP and also she'll be travelling on a different passport than usually (as her usual passport is with the Home Office). I know you can enter the UK without your BRP, it'll just be less convenient.

Now the questions are: Which way would be the best and most convenient to re-enter the UK? What documents should we bring and did we forget anything crucial?

PS: Just to be clear: On both flights and throughout the whole trip to Europe we will be travelling together. We will also both queue together at UK immigration. Needless to say, we want UK immigration to go as quickly and smoothly as possible but we won't be under time pressure.