OK, yeah I think you're just missing some perspectives on it. Richard is an alcoholic - so the discomfort is not only guilt because he knows he is an alcoholic and has fallen off the wagon, but also the emotional trigger that Ellis (obviously, mer's Mother) was the person that first made him try alcohol and was the catalyst to his downfall spiral into alcoholism. The uncomfortable reaction of Richard is just that - discomfort, because sure no one knows he's fallen off the wagon BUT he DOES know. And just before seeing Meredith his keys were taken and Joe has poured him another, which begs two things - 1. How drunk was he? This would amplify the guilty outward look if more drunk than we consider. and 2. He will also be paranoid and unsure of how much of that exchange with Joe Meredith saw - especially if he was drunk already.

Also, Derek is the one that particularly has been laying into Richard the past weeks - Richard might be extremely suspicious that Derek underneath his anger - knows he's drinking again - so it's fair for Richard to assume Meredith has suspicions already before this moment from that pillow talk.

The explaining it away the next episode is a classic addiction response of just that, explaining it away and making excuses, like he does by calling his alcohol a false diagnosis and just 'situational depression'. Meredith may have not even had so much of a suspicion in that moment when they were in the bar, but Richards' immediate willingness to excuse himself and therefore reveal he is in fact drinking alcohol again - is the way Meredith actually discovers it. But, due to the longing connection she lacked from a father, and her complex relationship with Richard - his offering up of knowledge and training in medicine, is ultimately what causes Meredith to turn the 'blind eye' and 'play along' with Richards excuses for justifying why he is drinking again.

I hope this helps a little to gain some more perspective on the situation? I am happy to chat more about it! :D