For anyone still needing help with this issue, I've just found a workaround.
While QuickTime 7 and MPEG Streamclip under El Capitan can no longer open mpeg-2 files, although there is an AppleMPEG2Codec.component from 23 August 2015 (v1.0.2) in System/Library/QuickTime, the regular QuickTime Player (v10.4) can.
So I opened the mpeg-2 file with the QuickTime Player and then did a Save as a .mov file. Although it was a 94 minute long feature film (1024x576), this only took some 15 seconds. The saved format was "'mp2v', 720 × 576 (1049 × 576), Millions MPEG Layer 2, Stereo (L R), 48.000 kHz". This new .mov file could then be opened by both QuickTime 7 and MPEG Streamclip. However, neither my old but still functioning Final Cut Pro noir Handbrake understands the mp2v format.
I then tried something different: I noticed that in the other library (the by default hidden user library) i had an AppleMPEG2Codec.component dated 31 July 2016 (also v1.0.2). So, I replaced the 2015 one in the System library by doing an ALT drag copy (so I wouldn't loose it if it didn't work), the system told me that an older version existed, I said replace and was asked to validate with my password, and then it replaced it.
When this was done, I once again tried opening the mpeg-2 file with MPEG Streamclip and QuickTime 7. It was still not possible, but the regular QuickTime Player could - and could save it as a .mov file.
So, my conclusion is that no matter how you do it, MPEG Streamclip and QuickTime 7 can no longer access the AppleMPEG2Codec.component. However, the regular QuickTime Player can - and it very quickly converts the mpeg-2 file to a .mov file which MPEG Streamclip then can open. Problem sorted, although it requires one extra step each time.
The big question is how long MPEG Streamclip will continue to work, as it's no longer supported. I have therefore started to look for replacements, and right now MacX Video Converter Pro is the best replacement I've found. It can handle mpeg-2 and is much, much faster than MPEG Streamclip. The settings are quite different, so it takes some time to get used to, but it's quite versatile. It turned that 94 minute mpeg-2 into a usable (i.e. editable in Final Cut Pro) h264 .mov file in four minutes. Converting a 94 min film from mpeg-2 to .mov in MPEG Streamclip would have taken some 30 minutes.