I think there are many, many reasons why High Lamas are keeping quiet on this issue.
Actually, some Lamas have already spoken on the issue like Geshe Kelsang, Gonsar Rimpoche, etc.
One of the reasons for not actively/openly engage the DL on this issue might be that High lamas will not engage in that sort of stuff (activism) anyway, no matter what the issue. Keeping the pledges of Mahamudra requires non-action, non-production. Many high Lamas speak very little, and do very little anyway (beside pure/clean dharma!).
The other thing is that explaining that 'relative suffering might (will) ultimately bring benefits' cannot be said because it cannot be defended by reason alone (hence it belongs to the metaphysical order of explanations). This is surely the case with DS as it has been written that attempt to eradicate him only made him stronger, more powerfull. Since we are innocent of what we are being accused of, this persecution will only bring benefits in the long term for us and the Gelug tradition. This is what high lamas call 'the power of truth'! So the persecution is good in the end, but that cannot be said, right? We cannot explain it to common sense.
Another thing is that if you really go down the road of replying to lies and deceit, in order to match your opponents' arguments you will be forced to escalate and say things like:
'Even the Dalai-Lamas visualises himself drinking blood and eating human intestines everyday (Argham, Padyam, etc.)' and 'What demon? The Dalai-Lama himself whorships Kali, the blood-thirsty goddess of death (Pelden Lhamo)!' If we want to match the rethoric of our opponents we will end up in these types of horrible debates opening the door to many, many broken samayas and suffering. It's a good thing our fathers didn't go down that road and showed a good self-restraint example, like lojong, etc.
So, I think there are many, many reasons why high Lamas did not bother replying, many of which are higher metaphysical reasons that translate very poorly to common sense (they have a bad 'media' value). Like one day, a high lama said: 'if tulkus didn't have faults we wouldn't be able to see them!' Well, I can understand the principle of the utterance. However, someone else, like someone very new to buddhism, might be shocked at this 'license to kill'! This could mean,'whatever they do is fine', like abuse, stealing, etc. Some utterances are better left with no debate or no answers because debating these statements 'rationnally' only brings more confusion and more questions and problems.
See the Trimondi's critizing of the DL and the Kalachakra tantra of an example of 'debating with reason' gone astray:
http://www.trimondi.de/EN/deba03.htmlTo avoid futur 'Trimondis' to 'reason' with our DS practice, it's better to keep a low profile, until the predicted sunshine, No?