Did you file a bugreport on this? Which widget and/or what was the cause? Details (link to bug-report to start with) please.

To topic:

1. For starters
hildon-desktop has nothing to do with widgets, all widgets run within hildon-home. The difference?! hildon-desktop is everything but what you can add to your desktop, means app-starter, status-tray (don't know if the menu is extra but its def. not "home"), operator name, clock, theme, 4 desktops and all transitions that come with it. hildon-home is just what you can add to your desktop or lets call it home screen in this case, means shortcuts, bookmarks, contacts and widgets displayed on your 4 "home"-screens.

2. Explanation
What causes your widgets disappear is that they make one of the native-widgets crash-loop (afaik), this results in a fallback where all widgets are reset and only the native-widgets are loaded again.

3. Warning
A widget which causes another widget to crash while under same process may crash something else if not unloaded at that time because its not in any process structure watching it.

Just an advice from someone who suffered from the beginning:
Banning all python widgets from hildon-home and with it python-loader; hildon-home seems much more stable to me. Before I did remove all that python stuff I could set a clock by crash-time. Keep in mind that fighting symptoms will never eliminate the cause.

You mentioned the mediaplayer:
Since PR1.2 mediaplayer's play button behaves normal and as mentioned in the bugreport this is not related to hildon-home problems only, however restarting it from the unresponsive state (remove and add again from home) makes 3rd party widgets disappear what is not a must to be connected, maybe the mediaplayer widget on itself starts a crash-restart cycle as it could not connect to services and a restart of the widget engine solves it's cause which automatically results in unloading of 3rd party widgets.

Overall I think it is a really bad idea to separate/cut out hildon-home processes. A good idea is to improve debugging output instead! This would help users to file better bug-reports and provide a better testing environment to developers.