Why don't you ask her if she could bear to live with it? she might prefer not to live with the disruption whilst pregnant, in which case your theorising is pointless. Equally, if she's struggling to pay the rent now, is there much point offering to keep her on during the work if you are planning to raise the rent afterwards?
Also, will it really take only 3 weeks and all go though the roof? It sounds incredibly quick and easy if so, but what if the weather is bad etc?
As a tenant, our landlady wanted to replace some flooring because the insurance was paying up; it wasn't necessary to do it then, and we asked her not to. She told us it would take 1 day. In the event, because of various unforeseen complications, it ended up taking 2 weeks, during which time the entire downstairs was out of order (everything from the kitchen/utility had been moved into the living room, so we had no kitchen/utility and no living room for 2 weeks!). It was a complete nightmare and she offered us no recompense at all. I certainly wouldn't be happy if a landlord wanted to get major work done while I was in situ - it is incredibly disruptive.
I can see that having an extra room afterwards might well make the tenant view the inconvenience as worth it, though. Why don't you explain you want to get it done, don't mind if she stays (though she may choose not to for above reasons anyway), and then it's up to you what recompense you offer. Some kind of recompense for the inconvenience seems fair - reduced or no rent whilst it's being done, and/or an extra room for free afterwards.
I suppose the thing is, she is doing you a favour too if she continues to rent during the (pretty disruptive) work, as you avoid void periods and the expenses of a new tenancy. Whether you are doing her an equal favour depends on how much she values having an extra room versus the hassle of living there whilst the work is done. I suspect if you're offering her nothing more than a few weeks of cheap/reduced rent in return for major hassle, followed by an increased rent she can't afford anyway, it's not going to seem terribly appealing to her. If the rent is going to go up after those few weeks, I'd imagine she'd wish to move out anyway, unless your rent is currently very competitive. Then again, if you're happy with her moving out, that needn't matter.
Finally, as I said on another thread, I do think that where you have a heavily pregnant tenant, it is reasonable to have some (human) consideration for that - would you want to be about to have a baby whilst living in a building site? It may be she doesn't mind, in which case well and good, but I think you should consider this when deciding about timings or the need to have the work done at all.