Cheaper labor is why you'd want an independent mechanic. On larger jobs that can mean it takes longer till completion but this work only takes a few hours and frankly it goes faster if done in one shot so it's still fresh in your mind the order in which parts came off and go back on. A shop may charge $100/hr but the mechanic typically gets half that (depending on skill level).
We would be guessing and making too significant a decision for you to tell you which to do, the smaller repair or keep going. If it NEEDS the lower gasket done and you only replace the upper, the work is somewhat wasted as it has to be torn apart again. The plastic upper manifold can be reused, and "probably" be able to reuse the new upper gasket, throttle body gasket, and "maybe" injector o-rings (lower O-rings, top will still be in place between the injector and fuel rail so usually don't need replaced, but could be prudent to replace *if you're keeping the vehicle long term*). To be clear, all three of these should be replaced with either repair. Whether they come with the upper manifold or not, determines whether they have to be purchased separately, same as whether they come with a lower manifold gasket kit but they usually do with the lower (which is what makes it a kit instead of just lower intake manifold gaskets).
Replacing the lower even if it isn't leaking would be prudent if you hope to keep the vehicle as long as possible. There are some variables to this, not only your preference but whether there was any significant wear running without oil. If the engine is in good shape, and depending on what it is and mileage (???????!!!!!!!!!!) it might last several more years, outlast the transmission which could be what totals the vehicle (unless a texting teen runs into you first). It could have a timing chain that's expensive to replace and soon to fail. We don't know the history of the vehicle or even which vehicle it is which is why the specifics and asking in a forum specific to that make and model of vehicle is usually the best way to get advice from fellow owners who have already gone through the same situation.
Similarly there may be other parts which are only accessible while the upper intake is off, or at least much easier to get to, things that may not be needed today to keep it running but are parts expected to wear out eventually, especially if they're the factory parts, things like temperature sensor(s), thermostat, and more depending on the engine (???????!!!!!!!!!!).
One way to do it is that the mechanic is examining everything while doing the work, and has plenty of light to see well. If while doing the upper, the area of the leak is found (which seems like it might have been, but that was something I was questioning earlier due to the details about leakage which didn't make sense as air is the primary thing that would leak from the upper gasket failure unless you're losing coolant) and there is reasonable confidence that's the only problem, then there is no cause at that time to do the lower if the only goal is keeping it running now as cheaply as possible. If no leak is found then the best long term strategy is keep going, taking the lower manifold off looking for the leak and this necessitates replacing the gasket to put it back on. "Most* gaskets will need replaced after they've been taken off after an extended period of being compressed. Some may need replaced after being installed and compressed even for a moment before being taken off.
That's about all I can tell you without being there and doing it myself. There's no way I can place a value on the vehicle working, how much money that would save you vs how much you like it vs body rust vs when other repairs might need done. For example if it's never had the exhaust done and you live in an area where it snows or rains a lot, that may be another few hundred dollars repair looming in the future. If the tires are bald there's another few hundred, and yet any vehicle eventually need new tires. You have to take it on a vehicle by vehicle basis.