That Skype might be backdoored has long been a concern. See link below.
I also noted in a past review I did that the official, independent crypto review and the description gained by a reverse engineering team differed significantly. The latter had design flaws and working exploits. Also, Skype's network controls the encryption keys so it must be assumed they have access to your calls.
The acquisition by Microsoft isn't a huge risk, I don't think. I do say, though, why take the chance if there's alternatives to Skype? Some are listed below.
Zfone. The ZRTP protocol underlying this protects end-to-end and has better security outlook than most others. This can work with (compatible) VOIP clients. (Jitsi supports it, for instance.)
Softphone with built-in crypto. It may or may not be very strong. However, if it's end-to-end, it's still more private than skype. (PhonerLite, TiviPhone, OctroTalk are examples)
Redphone on Android or similar free/commercial option for encrypted voice on mobile.
One of the earlier methods of protecting Internet voice was simply running it over a VPN or link encryptor. So, you might be able to work out a VPN setup with server/host on your network and a simple client for them to use. Then, they can connect and run voice call through it. Above options sound easier, though.