We are set on the first name [name_f]Willow[/name_f] for our girl and would really like to honour my grandmother by using her first name [name_f]Lilja[/name_f] (pronounced [name_f]Lily[/name_f]-ah) as the middle name. Thoughts on whether the alliteration is too much?
I think it sounds lovely- there is no alliteration. The repetition of the ‘l’ sound makes a link between the two names, without it being matchy. Good luck :).
Personally, I think this name is absolutely beautiful. The alliteration gives it a lovely sound and to my ears at least it sounds wonderful 
[name_f]Willow[/name_f] [name_f]Lilja[/name_f] is really sweet! And I love the meaning behind [name_f]Lilja[/name_f] (honestly, I just love [name_f]Lilja[/name_f] period! Then again, I seem to have a thing for Polish/Eastern European spellings rather than the original–like Gracja, Lilija, [name_f]Walentyna[/name_f], etc.!). I think [name_f]Lilja[/name_f] [name_f]Willow[/name_f] sounds much better–there’s more distance between the "L"s, and I love seeing [name_f]Lily[/name_f]-anything up front, and I think [name_f]Lilia[/name_f] [name_f]Willow[/name_f]/[name_f]Lilja[/name_f] [name_f]Willow[/name_f] sounds amazing, but I wouldn’t try and keep you from your number one or anything. 
I think the sounds are indeed very repetitious, but I also think the significance of [name_f]Lilja[/name_f] trumps flow here. They’re both gorgeous names!