Is this really the expected behavior? I thought we wanted to avoid having destructive actions as a default? Once the data is imported, it's near impossible to cancel the merge.

Yeah, Chris and I discussed this at length when designing these screens. Our reasoning was:

1) If you're just switching your sync accounts, you're likely to do so through the dedicated UI for switching sync accounts in sync settings. In that case, it certainly makes sense to have the default be "Keep existing data separate" for the reasons you mentioned.
2) Therefore, if you're signing out and then back in again with a different account, your likely not primarily doing so to switch sync accounts. Maybe you sign out, browse in a signed-out state for a while, get a new personal account, add it to your device, and sign back in with that account. Or maybe you just wanted to be signed out for a little while, and then decide to sign back in with a different personal account. Either way, if your only intention was to switch sync accounts, you probably would've just used the UI intended for that action (see 1).
3) Given (1) and (2), it's unclear exactly what the right default is. There are risks either way. One risk (if the default is "Import existing data") is that data may accidentally get merged into an account you don't want, and as you mention, that's a difficult action to undo. However, in the other direction (if the default is "Keep existing data separate"), there's a risk that we clear some browsing data that you generated while you were signed out (and thus was not synced to any account). That data is now impossible to retrieve, since it was never synced to another account and has been cleared from your local data.

Given these two risks, we felt the "riskier" one was accidental data deletion (erring on the side of preserving data felt "safer"). Thus, we thought "Import existing data" was a better choice.

I acknowledge both are suboptimal; hopefully users recognize that this is a tricky operation, and pick what makes most sense for their use case. Chris, feel free to add to that logic.

The following revision refers to this bug:
  https://chrome-internal.googlesource.com/chrome/ios_internal.git/+/1d4848e12ce61f3faa39f5874bbdb2db7516db54

commit 1d4848e12ce61f3faa39f5874bbdb2db7516db54
Author: bzanotti <bzanotti@google.com>
Date: Wed Mar 23 10:15:03 2016

Verified the issue in the latest build 51.0.2693.2 dev tested on iPad(iOS 9.2.1).
Import existing data" option is checked by default on switching the accounts, looks good.

Just to clarify: it's only checked by default when switching accounts by signing out and back in again, correct? "Keep existing data" should be checked by default when switching sync accounts via the sync settings screen (under the "Sync to" section).

Correct. :)

Great, thanks :)