Aye, it is hard to balance out. But look at it this way: presume for Missions, 1 Karma (1K) and 2,000 Nuyen are interchangeable.
The cost to initiate, if we are just buying quickening, is 13K. The cost to buy the spell in question, 500 Nuyen, 5K to learn it. Our total karma cost to quicken 1 spell is: 13+5+1, or 19K, or 38500 (500 nuyen for the cost of the health spell). For an Increase Attribute spell, we could increase, say, Agility, by +3 easily (Magic 6, Spellcasting 6). Lets also increase our strength, so that we can compare to used Muscle Replacement (the cheapest available option) and compare. We initiate again, for 16+5+1K, or 44,500 Nuyen plus our original 38,500 or 83000 total nuyen. A rating 3 Muscle Replacement, to give us the same +3 augmentation to Strength and Agility? 56250 nuyen 3.75 essence. I think that is roughly comparable, considering that initiating is giving you other benefits as well and makes up 58000 nuyen of that total cost. If you take Mentor Spirit (Bear), Specialization (Health) for spellcasting, you have 6+6+2+2, or 16, enough to buy 4 hits and get +4 to Agility and Strength for 83,000 Nuyen. Our used muscle replacements would run us 75,000 Nuyen and cost 5 essence. Even if we factor in the cost of the Mentor Spirit (10 karma, buying it after creation, and 7 karma for the specialization, for another 17 karma or 34,000 nuyen equivalent), we're comparing 117000 vs. 75,000 and 5 essence. We don't buy it used? 117,000 vs 100,000 (and 4 essence).
Quickening Improve Attribute spells is still a solid option, but its COMPARABLE to cyberware... not straight up better than it.
As far as quickening in play goes... nothing prevents you from, at the start of a mod, edge-casting an improve reflexes or combat sense spell and spending 1 karma (2,000 nuyen) to quicken the spell. You gain a massive bump, at the cost of 1K/2,000 nuyen, or roughly 10% of your final reward, but in most cases such a spell will be so absurdly powerful that it will provide you with an edge worth 10% of your final reward. You won't get to keep it for the next module, but for the module you play in it is still a valid option and still quite powerful.