I am as sad as most (all?) of you about this recent development. What I would hope for is that maybe(!) GA will, regarding the quality of the inflight product, sooner or later be able to fill the gap in ST that we would have expected/hoped MH to fill.

If GA grows and expands its network, travel to Australia might even become better than now because flights would be on Skyteam entirely. With the current QF/AF codeshare flights, for example, you frequently have big discussions with QF staff as to whether or not, and if so: to which extent, FB status has any consequences.
Looking a bit into the future, travel to Australia might, at some point of time, even go via both CGK and DPS. (GA already offers quite a few flights from DPS to Australia.)

And looking at the current MH/KL cooperation regarding flights to Australia, the situation is not very bright anyway because KL does not seem to be able to offer much capacity on the KUL-Oz routes. In recent months they would often try to sell you QF flights (no codeshare!) to SIN and then with KL from there, or, alternatively, flights on CZ. So if the MH/KL cooperation ceases to exist due to MH joining OW this is much less a loss for Europe-Australia trips than it might appear at first sight. (The same might apply to Europe-NZ.)

I am just trying to see something positive here. If I am right with what I just wrote, it might well be that in, say, 4 years, provided GA is to have a positive development, we will not see MH as a big loss anymore. After all, when looking at the past 10 years, you can conclude that ST has done quite a good job in choosing airlines with some potential for development.