Thinking some more on the recitation, I realize that while in modern Japanese lengthening the CV syllables to CV̄ causes massive mergers of C(y)o with Cō syllables, C(y)u with C(y)ū syllable and Ce with Cē syllable, if we go back to early middle Japanese, those issues are not there at all.
Modern day Japanese /ō/ derives from a shocking number of different sequences: au, apu, aũ, waũ, ou, opu, oũ, eu (> yō), epu (>yō). None of them, however, would have been homophonous with a short /o/ that was lengthened to [ō].
The same is true for /ē/ which either comes from ei or eĩ.
ū likewise can come from ipu, iũ and uũ.
As /ī/ and /ā/ don't really occur in Chinese nor Japanese vocabulary, lengthening these would not lead to big disagreements either. I thought it'd be fun to reconstruct the Heart Sutra in early middle Japano-Chinese pronunciation, with the short syllable lengthened to be metrically equivalent to Middle Chinese CvC syllables. So here it is:
仏説摩訶般若波羅蜜多心経
bussetsu(busset?) mākā pannyāpārāmītā sinkyaũ
観自在菩薩
kwanzizai bōsat
行深般若波羅蜜多時
gyaũ zin pannyāpārāmītā zī
照見五蘊皆空
seu ken gōun kai kuũ
度一切苦厄
dō issai kūyaku
舎利子
syārī sī
色不異空 空不異色
siki pū ī kuũ kuũ pū ī siki
色即是空 空即是色
siki soku zē kuũ kuũ soku zē siki
受想行識 亦復如是
zyū sau gyaũ siki yaku bū nyō zē
舎利子
syārī sī
是諸法空相
zē syō popu kuũ saũ
不生不滅 不垢不浄
pū syaũ pū metsu (met?) pū kū pū zyaũ
不増不減
pū zoũ pū gen
是故空中無色
zē kō kuũ tyuũ mū siki
無受想行識
mū zyū sau gyaũ siki
無眼耳鼻舌身意
mū gen nī bī zessin-ī
無色声香味触法
mū siki syaũ kaũ mi soku popu
無眼界 乃至無意識界
mū gen kai nai sī mū ī siki kai
無無明 亦無無明尽
mū mū myaũ yaku mū mū myaũ zin
乃至無老死 亦無老死尽
nai sī mū rau sī yaku mū rau sī zin
無苦集滅道
mū kū zipu metsu(met?) dau
無智 亦無得
mū tī yaku mū toku
以無所得故
ī mū syō tokkō
菩提薩埵
bōdaisattā (bōdisattā?)
依般若波羅蜜多故
ē pannyāpārāmītā kō
心無罣礙 無罣礙故
sin mū kē gē mū kē gē kō
無有恐怖
mū ū kū pū
遠離一切顛倒夢想
on rī issai tentau mūsaũ
究竟涅槃
kuũ kyãu nē pan
三世諸仏
sansē syō butsu (but?)
依般若波羅蜜多故
ē pannyāpārāmītā kō
得阿耨多羅三藐三菩提
toku ānokutārāsanmyakusanbōdai
故知般若波羅蜜多
kō tī pannyāpārāmītā
是大神呪 是大明呪
zē dai sin syū zē dai myaũ syū
是無上呪
zē mū zyaũ syū
是無等等呪
zē mū toũ toũ syū
能除一切苦 真実不虚
noũ dio issai kū sinzitu pū kō
故説般若波羅蜜多呪
kōsetsu pannyāpārāmītā syū
即説呪曰
soku setsu syū watsu
羯諦羯諦波羅羯諦
gyātei gyātei pārāgyātei
波羅僧羯諦菩提薩婆訶
pārāsoũgyātei bōdī sowakā
般若心経
pannyā sinkyaũ