I too am a conflicted on what to do about it. It seems we have three options:
1) Ignore it.
2) Craft amendment(s) to the BCO to make it more explicit.
3) Make a complaint (BCO 43) to the respective Session and then to Presbytery if the Session disagrees with the complaint.
I think 1) is no good.
Number 2 above has some merit. It will at least initiate a discussion in your Presbytery about the merits of women as deacons and could be passed and sent to GA. The downside is that the BCO is already clear, so it's kind of difficult to decide where to amend the BCO to make it say what it already says.
I would keep these rules in mind when crafting ammendments.
First, the simpler thae actual ammendment the better. The whereas statements can be as complicated as you like, but verbose and confusing ammendments will alone cause some to vote against it.
Second, If you want to make a change to more than one part of the BCO, then I would make those seperate overtures. If you lump them together, then you may get folks who vote against it because they find one part of the ammendment objectionable. The more seperate ammendments you have in single overture, the more negative votes might accumulate in this way.
Third, I would be careful which part of the BCO you ammend. For example, if you wanted to make a change to the BCO's definition of deacon, then put that in Chapter 9 or 7 which are purely definitional Chapters. If you wanted to make a change to the process of appointing deacons, then Chapter 24 is probably best. Some folks will vote against an ammendment if violates the current organization of the BCO.
Initailly, I thought option 3) might be the more contentious route to take and therefore less adviseable. However, Chapter 43 deals only with overturning the decision of one of the lower courts of the church. Chapter 43 in no way leads to charges or a case of process, so it's really not that contentious. The more I think about it, the more I see this option as being the best option. With this option, the problem could be fixed at Presbytery (or even at the Session level). If the Presbytery could not come to a general consensus, then they could reference (BCO 41) to GA. Whatsmore, if your Presbytery did not rule in your favor, you could still craft an overture for the next meeting of Presbytery.