What do you think about a short, single-target stun (0.5/1s) being applied if both 1's hit in a certain, short time interval? IMO, a bit more counter-play than your idea, but it still serves the same purpose I'd want (a means of protection via hard CC, along with the means of cancelling channeled abilities). If it's too much, maybe make the interaction go on a 10/15s cooldown so she can't perma-stun. I had thought about the method of execution applying different effect, such as dark 1 into light 1 being a 1s single-target stun, whereas light 1 into dark 1 being a tiny, AoE 0.5s stun, but that seems OP.
The idea came yesterday when reading through a bunch of old Hel threads and getting the consensus that she is too vulnerable to ganks/hard engage given her small health pool and lack of a hard-mobility ability (soft-mobility like her movement speed increase from her heal don't count). The anti-heal mechanics this game has to offer screws her over big time as well, but at least with a stun you can self-peel better when it's happening to you. I believe every God should have a weakness (or weaknesses) but not so glaring, and in multiple areas, as Hel does.
Back when I played a different MOBA, namely LoL, I played a character, very much like Hel, called Anivia. In order to get my point across, I will compare the two. Both Hel and Anivia are the squishiest mages of their respective games. Both Hel and Anivia are mana-hungry or even considered blue buff reliant early-mid on. Both Hel and Anivia are immobile, bursty-utility mages that must be mid-combat in order to get half their damage off. They're both rarely, if ever, seen in competitive play or even leagues/ranked... hell, even in casuals/normals they're not picked nearly as often as I feel they should be. They're both technically weak early-game but have unexpected dueling potential, if given enough mana and played right, in the laning phase, pre-ult. So what are their differences? Anivia can't heal but she has a 4/5 min cooldown revive passive (which can be denied), two forms of movement speed slows, Ymir's wall, and an unreliable 1s stun, very much like Isis' 2 (but slower), to provide self-peel. Even if you remove her revive passive, she can very much fend for herself if getting dove or getting ganked in the mid-point of the lane. When I play Hel I don't feel like her movement speed debuff, movement speed buff, cleanse, and heal can truly deter someone who wants you dead - especially when playing from behind. I love her (or both of them? ='P) to death though!