The current punctuation here in Alma 60:12 incorrectly breaks up this complex construction. The that after suppose is a subordinate conjunction; by placing a comma after the that, the 1830 typesetter made the that read like a pronoun. There is really no need for a comma after suppose that.
The more significant problem in this passage is that there are two occurrences of because but no finite verb; we therefore have a sentence fragment. For the 1840 edition, Joseph Smith eliminated the fragment by inserting it is before the second because. The editors for the 1852 LDS edition, following the 1840 edition, also added these words to the corrected plates for the second printing of the 1852 edition. Thus the current LDS and RLDS editions follow the 1840 emendation. In this instance, 𝓞 is not sufficiently extant for the word immediately following killed for us to be sure that it is was not originally in 𝓞. Only the beginning of the first letter of the following word is extant, and it could be either a b (for because) or an i (for it). As it is, there is not enough space in the lacuna of 𝓞 for the text of 𝓟 (the transcript for 𝓞 supralinearly inserts the their, for instance, but follows 𝓟 in assuming that there is no it is).
There are no instances elsewhere in the text of this kind of complex structure, namely, “suppose that because S it is because of NP” (here S stands for a finite clause and NP for a noun phrase). But we can find evidence for more general forms of this construction. There are, for instance, 89 examples of “suppose that S” in the earliest extant text, including one where the subject and main verb in the finite clause S is the existential expression it is:
The clause “it is because” is fairly frequent elsewhere in the text (occurring 15 times), with one clear example of “it is because of NP”:
And finally, there is independent evidence that a subordinate that-clause can start out with a subordinate because-clause, as in these examples:
Putting all these possibilities together, we can get “suppose that because S it is because of NP”, the structure for Joseph Smith’s 1840 conjectured reading here in Alma 60:12.
There is some evidence for the loss of it is elsewhere in the text. Here is one clear example:
A second example is conjectured:
(See the discussion under each of these passages.) So here in Alma 60:12, we may very well have another instance where it is was lost early on in the transmission of the text, in this case most likely when Joseph dictated the text to Oliver.
Another possible emendation in Alma 60:12 would be to remove the first because:
One could argue that the first because, partially extant in 𝓞, was accidentally inserted into the text as Joseph Smith dictated the text to Oliver Cowdery. There is one instance in the history of the text where Oliver accidentally inserted an extra because, although in that case it was a preceding because that prompted the repetition, not a following one, and the insertion occurred during the copying of the text rather than during its dictation:
Moreover, this particular error in 𝓟 was only momentary. On the other hand, the evidence for the loss of short existential expressions during the early transmission of the text is stronger. For some other examples (such as the loss of these are and there was), see the discussion under Alma 58:33. Here in Alma 60:12 it seems more likely that during the dictation of the text it is was accidentally lost than an extra because was inserted. Ultimately, the earliest text for Alma 60:12, given its two instances of because without any verb, seems quite unacceptable. The most reasonable emendation appears to be Joseph Smith’s conjectured it is.
Summary: Accept in Alma 60:12 Joseph Smith’s conjectural emendation that added it is to the impossible earliest reading (giving “do ye suppose that because so many of your brethren have been killed / it is because of their wickedness”); another possible emendation would be to remove the first because (giving “do ye suppose that so many of your brethren have been killed because of their wickedness”).