some Embassy still OK, like KL or Yangon, but the other issue will be airport entry. So everyone should make a proper plan. I just encounter a sad story with a Turkish lady.
the problem at the moment that even schools can not be sure about which place is gonna accept. We have a real nightmare with ED applications. It's like rolling a dice or worse.
You are lucky, Malaysian can enter Thailand unlimited times, just POI PET (Aran) is not the best place to do border run. Do it in Ban Laem, Ban Laem or Kanchanaburi.
Have your wife go to Immigration, after a certain time your wife can file an appeal that you allowed back to stay with your family. Lawyer can not help. Let her go direct to IDC, there is a small Office where she can file the appeal. The Officers are helpful as long as no drugs involved. The appeal is THB1900, no need to pay extra,