Pulling Alan out of the story at this point makes sense, regardless of where the story is headed next there's about 0 tension left anymore in the short term. The empire is now obviously by far the strongest force on the planet and the bugs are potentially hundreds of years out so something has to fill time here. Outside of some complete switch in direction like fighting an evil god or something there's only really few ways to move forward at this point. You either kill Alan off or more likely put him in some cryopod so he can keep popping up later in the series and maybe show up in the finale and then do one of these things:
A) you end the series with some montage style view on the planets development, show how few of the characters did and how Alan's line does perhaps ending in the bugs attacking and being repelled as a sort of couple chapter send off to the series.
B) continue into the next story arcs as usual that basically follow A's story but flesh it out with several full arcs and multiple characters with time skips between major events. For instance we could have an Cleria arc here on how she handles things without Alan, then some post Cleria internal division arc where Alan's grandchildren fight it out between themselves when Cleria dies and then few more arcs in same vein with some kind of crisis that disrupts the plan (people losing faith in the bug killing mission, a civil war etc.) and how it's resolved, bit like how Foundation books go really, which then again ends when the bugs show up and get defeated. Alan can come up from the pod every now and then in this scenario, play the part of Hari Seldon dispersing wisdom and restoring faith in the mission before going back to cold sleep. If they really wanted they could invest into this whole humans turning into bugs thing too, perhaps as one of the later arcs or as the final arc post bug contact.
I could see either one happening, or really B pivoting into A as soon as the sales drop off. I suppose it ultimately depends on the series sales.
I really hope this isn't setup on Alan being the gods emissary and then fighting an evil god though but I give that solid 5% chances too.