Of course it's really silly that they fitted the new clutch without addressing the issue of the oil leak. Any oil inside the bell housing should immediately flag up that additional action is needed. Even the smallest of leaks from the input shaft seal is unacceptable as it'll always just get worse with the result you've experienced. They should have left you in no doubt that this issue needed to be addressed.
Having said all that, leaks from the input shaft on our gearboxes is not all that uncommon, seems to be a wee bit of a weak point on them. Also seems to be often accompanied by detectable wear in the first motion shaft (input, splined , shaft you can see) bearing so it's just as well the seal is integral with the bearing and you can't do just the seal on it's own. The bearing and that splined shaft can't be extracted into the bellhousing which is why the box needs to be dismantled, to allow the shaft with it's bearing to be removed. Luckily I've never had to do one and I know the "official" way to do it is to remove the casing entirely and then the gear clusters - quite time consuming - However I've seen videos showing how you can do it without completely dismantling the box which look very "doable" but probably not for the faint hearted to attempt. Maybe the video guide Panda Nut mentioned above shows this procedure? I must have a look for it.
In your situation I think you need to consider
1. Carrying out the actual replacement of the clutch itself is not a very difficult operation - you don't need to be a "super tech" for a job like this so even someone not all that proficient should be able to achieve a good out come.
2. When you got the car back with the new clutch fitted it worked Ok I think? So it looks like they got the job done well enough - what went wrong was that, for whatever reason, or incompetence, they failed to properly take into account the ongoing effect of the oil leak and impress on you the need to attend to this which resulted in your present situation.
3. - and this is the biggie, They are not going to be the ones who are working on the gearbox to rectify this leak/bearing problem. As this leak/bearing problem is not exactly an unknown one, anyone specializing in gearbox repair will be familiar with it and with this gearbox, so the likelihood is that the "specialist" will do a good job in this respect leaving the garage with the job of just doing the clutch which is a job many DIY driveway grease monkeys manage to do very satisfactorily.
4. I presume the garage and gearbox specialist will warranty their work? So if it all doesn't work out it should then be covered by their guarantee - I'm thinking especially of the gearbox repair. But that's the pessimistic side of me showing through! Get the seal bearing sorted out and all should be well.
So I think that, if it was me, I'd just authorize the gearbox repair and feel moderately confident that the issue will thus be sorted. I think this is probably the best and most cost effective thing for you to do - or, if you're totally lacking in conscience or scruples, just get them to clean up the flywheel, pressure plate and inside the bell housing with a good soaking of something like brake cleaner - None of these parts are worn in any way and couple of spray cans would probably make a good job. Then slam it back together with a new driven plate (friction lining - because you can't effectively clean up heavily contaminated friction material) Take it home and don't drive it at all and either part ex it for another car or sell it privately. Unless you renew that seal/bearing it's only going to be a matter of days, possibly weeks, before you're back in this situation again.
You're in a horrible situation here and my heart bleeds for you - hope it all comes out well in the end whatever you decide to do.
