However before we get to analyzing the answer lets have a quick look at how the Ha'aretz translators summarized the answer:
"The text attributed to Eliyahu urged revenge against secular Jews, calling on people to attack them, smash their heads in and bring their children back into the religious fold. "Ha'aretz yet again demonstrate that their translators have no understanding of spoken Hebrew. The phrase להסתער עליהם, לטחון להם את הראש would if translated word for word using only a Hebrew-English dictionary mean roughly what Ha'aretz ascribed it. However, we do expect translators to have some basic understanding of the language they are translating beyond using a dictionary. In spoken Hebrew the phrase להסתער means to do something with enthusiasm. לטחון את הראש is usually used in the negative sense to mean to bring something up again and again to the point of being a nuisance. Together, the entire pharase would mean that you should go with enthusiasm to Hilonim and talk/argue with them to the point of being a nuisance. I.E. work really hard at convincing them to do Teshuvah.
**Late Edit - After I pointed out the error on Twitter, Ha'aretz swiftly corrected their translation.
OK, now that we've removed the bizarre interpretation given by Ha'aretz translators, lets try and understand what Rav Eliyahu actually said. When you read the text carefully, Harav Shmuel Eliyahu only really says two things. One - you should get revenge on the non religious. Two - that revenge will be by making them or their children do Teshuvah (I.E. become religious). That's it. The text is not as bad as some people are interpreting it. However, it is bad enough. I don't think any real rabbi would object to a general aim of making all the non religious do Teshuvah. However, Rav Eliyahu is not talking about a process that comes out of a deep love for all of Israel. What comes across quite clearly is that Rav Eliyahu sees all the non religious as the enemy. They need to be conquered. Just as troubling he is convinced that no one could be religious and approve of the disengagement. That is because for him there is only one legitimate religious position - a far right one.
A Chief Rabbi can not see the majority of the nation as enemies. The Rabbanut is already hated, and needless to say this kind of rhetoric will not make it any more loved.