The "no" above was in reference to exactly that. I don't think we'll see "estimated at" in a correct answer. However, English is tricky--it depends on the intended meaning. We certainly can't say "estimated at X years old." The idiom is "estimated to be." But what about something else? I could imagine a sentence that said "The damage was estimated at $45 million dollars." This makes more sense than "to be," since a rock sample can BE millions of years old, but damages can't BE millions of dollars. Rather, millions of dollars in damages occurred.

Having said all that, I don't have an official SC question to validate that usage for the GMAT. If anyone can find a correct official answer with ANY use of "estimated at," I'd be interested to see it.
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Main Issues:

1) SV: "Samples...have"
2) Correct Idiom: "dated at"

(A) has been dated to be 3.47 billion years old and thus is - Wrong: 1) SV 2) Idiom
(B) has been dated at 3.47 billion years old and thus - Wrong: 1) SV 2) Structure
(C) have been dated to be 3.47 billion years old and thus are - Wrong: Idiom
(D) have been dated as being 3.47 billion years old and thus - Wrong: 1) Idiom 2) Structure
(E) have been dated at 3.47 billion years old and thus are - Correct

907. Rock samples taken from the remains of an asteroid about twice the size of the 6-mile-wide asteroid that eradicated the dinosaurs has been dated to be 3.47 billion years old and thus is evidence of the earliest known asteroid impact on Earth.
Meaning:
Rock samples taken from the remains of an asteroid about twice the size of the 6-mile-wide asteroid = ->So some rock samples were taken. No verb for plural subject Rock Samples till now
that eradicated the dinosaur
“That” is referring to asteroid. Asteroids eradicated the dinosaur. No verb for plural subject Rock Samples till now
has been dated to be 3.47 billion years old
This is the verb for the plural subject rock samples. A singular verb has been dated. SV pair error exist.
Not eliminating on basic of any idiom usage here but “dated at” is correct. “Estimated at” and “Estimated to be” is acceptable
thus is evidence of the earliest known asteroid impact on Earth.
Again singular “is” for plural subject Rock Samples
Finally meaning,
The rock samples Has been dated … and Is evidence …
Error:

(A) has been dated to be 3.47 billion years old and thus is
Error as pointed out
(B) has been dated at 3.47 billion years old and thus
Same error as pointed out also missing verb after “thus”
(C) have been dated to be 3.47 billion years old and thus are
Seems fine. Original doubt exists on idiom “dated at vs dated to be”
(D) have been dated as being 3.47 billion years old and thus
As being is incorrect to use with dated
(E) have been dated at 3.47 billion years old and thus are
Seems fine. Original doubt exists on idiom “dated at vs dated to be”

C vs E, comes down to idiom usage only. So going by what we know “dated at “is definitely correct usage as we would have heard at many occasion.
So correct answer E.

Rock samples taken from the remains of an asteroid about twice the size of the 6-mile-wide asteroid that eradicated the dinosaurs has been dated to be 3.47 billion years old and thus is evidence of the earliest known asteroid impact on Earth.

(A) has been dated to be 3.47 billion years old and thus is
Has is incorrect with “Rock samples”.
“is” is incorrect here. Requires “are”.
Correct Idiom – “Dated at”

(B) has been dated at 3.47 billion years old and thus
Has is incorrect with “Rock samples”.
Rock samples …thus evidence. Helping verb is missing.

(C) have been dated to be 3.47 billion years old and thus are
Correct Idiom – “Dated at”

(D) have been dated as being 3.47 billion years old and thus
Rock samples …thus evidence. Helping verb is missing.
Correct Idiom – “Dated at”

(E) have been dated at 3.47 billion years old and thus are
“Dated at” is the correct idiom.

OFFICIAL GMAT EXPLANATION

Agreement; Idiom

The plural subject of this sentence, Rock samples, requires plural verb phrases—have been dated and are rather than has been dated and is.The idiomatic way of expressing estimation of age is with the phrase dated at.

A The subject and verbs do not agree; dated to be … is not idiomatic.

B The subject and verb do not agree; the conjunction and thus should be followed by a verb.

C Dated to be is not idiomatic.

D As being is not idiomatic; the conjunction and thus should be followed by a verb.

E Correct. The plural verbs match the plural subject, and the wording of the sentence is idiomatic.

The correct answer is E.

Rock samples taken from the remains of an asteroid about twice the size of the 6-mile-wide asteroid that eradicated the dinosaurs has been dated to be 3.47 billion years old and thus is evidence of the earliest known asteroid impact on Earth.

(A) has been dated to be 3.47 billion years old and thus is-> Subject verb agreement issue. We have "rock samples"(plural). has is incorrect.
(B) has been dated at 3.47 billion years old and thus-> Subject verb agreement issue. We have "rock samples"(plural). has is incorrect.
(C) have been dated to be 3.47 billion years old and thus are-> "dated to be" is incorrect.
(D) have been dated as being 3.47 billion years old and thus-> "as being" is incorrect.
(E) have been dated at 3.47 billion years old and thus are-> It is better.

So, I think E.