I used to follow this issue, but haven't for a while. I just glanced at the law, and it appears that the law has indeed been amended as you point out. Below is a translation, found online, of the current Article 25 of the Immigration Act.
Article 25 An alien, who has legally and continuously resided in the State for five (5) years and for more than one hundred and eighty-three (183) days each year, or the alien spouse and/or children of a national with registered permanent residence in the Taiwan Area who have legally resided in the State for ten (10) years, during which period they have actually resided in the State for more than one hundred and eighty-three (183) days each year for five (5) years, may apply to National Immigration Agency for permanent residence if they meet the following requirements. The foresaid periods shall not include the period of staying (residing) in the State by any of those aliens whose residence in the Taiwan Area is permitted due to studies or employment in the Taiwan Area as approved by the central authorities in charge of labor affairs or the field of their employment pursuant to Subparagraphs 8 to 10, Paragraph 1 of Article 46 of the Employment & Service Act.
1. Are at the age of twenty (20) or over.
2. Have a decent character.
3. Have considerable property, skills or talents that enable them to make a living on their own.
4. Are beneficial to the national interests of the State.
The amendment to this article was introduced in Dec. 2007. (The former relevant article was Article 23.)
In my reading, the law is indeed somewhat gray on this point on its face. It would be interesting to look at the legislative comments and see whether they clarify anything. The fact that the legislature specifically removed the 5 years continuous residency for spouses provision is disturbing for people in your position. However, it could be that -- in tandem with lowering the threshold for non-married applicants from 7 to 5 years -- they were simply streamlining the wording of the law (in which case married applicants might still be allowed to apply under either the "continuous 5 year" or "5-of-10" criteria). I can't t currently offer any more of an answer on this. Let us know what you learn.
[Edit to add:
Okay, I found a copy of Executive Yuan comments on a draft bill of this amendment, here: http://www.ey.gov.tw/public/Attachment/15510452971.doc
The comment on the relevant paragraph 1 of Article 25 says only that the amendment is a revision to the "wording" of paragraph 1. I think this may be grounds for cautious optimism that the substance of the former provision that would allow you to be eligible at 5 years should still apply. I certainly can't guarantee that the immigration authorities will see it that way though.]