While I'm not in a progression guild, we have our share of managing our time as well considering we only raid about 6 hours a week. That said, and this will depend solely on the culture of your guild:
You could ask your raiders where their goals lie.
Do people want to farm gear to fill their slots? Maybe poll for a list of gear that people need, drop the minority bosses, and shift the schedule around that.
Do people want to progress, and don't feel like loot is an issue? Then drop the finished bosses unless you have them down pat, and set a goal on what to work on every week.
If no one shows for a farm night, it sounds to me like people don't have the time, or loot isn't important to them. To be honest, in my opinion, you should be talking to your guild about what they want to accomplish, and not asking strangers. Have you polled your group to see how many people can/want to be on? I think you need the pulse of your group, and work with them. It would be a happier group I would think.
It depends what pieces people are missing,....if they're waiting on a ring or neck or some small upgrade like that then obviously that should not warrant wasting time on farm. But if half the raid are missing weapons and/or trinkets or something huge like that then a second look should be given. I know my dps went up by almost 4k when I got my Sha weapon.
We raid 2 nights, and we have also had to make choises. (We're currently close to killing Sha on normal). The lack of time to clear content is a big big constraint on our progress.
Around the time we got to kill Garalon we did one more MV run, where we swapped an alt in for Spirit Kings. So that alt was then saved to a 4/6 lockout, and in subsequent weeks we used that alt to kill Elegon and Emperors directly, leaving the first four. We only did this for 2 weeks though, when we permanently dropped MV from our schedule to fully spend in HoF.
We've extended 2 raids i think to spend fully on Empress, ignoring possible upgrades but we just needed time for progress tries.
Now we've saved that same alt to Garalon's death, so we only need to kill the 3 bosses with tier tokens, and we dont kill the first 3 anymore. TES is 4 easy bosses so will not skip there I guess.
After Sha is dead I think we will spend (part of) 1 night on TES and the week after on the end of Hof, and spend the other night on MV Heroic. So alternating those kills for Valor and Tiertokens/sha weapons.
We usually skip Vaults most of the time, few people in our roster still has major upgrades from that place and we find doing the farm in HoF and focusing on progress after HoF is done to be more worthwhile.
We do farm content on an off night.. (3d raid weeks.. 2.5h a night)
We can clear HOF and ToES in 1 raid night no problems.
It's just about managing and having no downtime.. Make use of your raid.
4 Hours is a long raid night.. Make best use of your time, and have a small 10 min (not a sec later) break mid way though your raid, keep everyone refreshed.
We manage 16/16H + alt run full clear of normals + few heroics. Doesn't take too long
We do MSV with ~18 mains and 7 alts. Loot train the alts. After that we go into MSV with ~18 alts and 7 mains. We do 5/6H.
Likewise with HoF, mains + few alts, then alts + few mains. Couple hardmodes in the alt run.
We start with Terrace>MSV Main>MSV Alt>HoF Main>HoF Alt>Terrace Alt